Kringles are autonomous structural domains, found throughout the blood clotting and fibrinolytic proteins. Kringle domains are believed to play a role in binding mediators (e.g., membranes, other proteins or phospholipids), and in the regulation of proteolytic activity [, , ]. Kringle domains [, , ] are characterised by a triple loop, 3-disulphide bridge structure, whose conformation is defined by a number of hydrogen bonds and small pieces of anti-parallel beta-sheet. They are found in a varying number of copies in some plasma proteins including prothrombin and urokinase-type plasminogen activator, which are serine proteases belonging to MEROPS peptidase family S1A.

Steroid or nuclear hormone receptors (4A nuclear receptor, NRs) constitute an important superfamily of transcription regulators that are involved in widely diverse physiological functions, including control of embryonic development, cell differentiation and homeostasis. Members of the superfamily include the steroid hormone receptors and receptors for thyroid hormone, retinoids, 1,25-dihydroxy-vitamin D3 and a variety of other ligands []. The proteins function as dimeric molecules in nuclei to regulate the transcription of target genes in a ligand-responsive manner [, ]. In addition to C-terminal ligand-binding domains, these nuclear receptors contain a highly-conserved, N-terminal zinc-finger that mediates specific binding to target DNA sequences, termed ligand-responsive elements. In the absence of ligand, steroid hormone receptors are thought to be weakly associated with nuclear components; hormone binding greatly increases receptor affinity.

NRs are extremely important in medical research, a large number of them being implicated in diseases such as cancer, diabetes, hormone resistance syndromes, etc. While several NRs act as ligand-inducible transcription factors, many do not yet have a defined ligand and are accordingly termed 'orphan' receptors. During the last decade, more than 300 NRs have been described, many of which are orphans, which cannot easily be named due to current nomenclature confusions in the literature. However, a new system has recently been introduced in an attempt to rationalise the increasingly complex set of names used to describe superfamily members.

Patthy L. Evolution of the proteases of blood coagulation and fibrinolysis by assembly from modules. Cell 1985 Patthy L, Trexler M, Vali Z, Banyai L, Varadi A. Kringles: modules specialized for protein binding. Homology of the gelatin-binding region of fibronectin with the kringle structures of proteases. FEBS Lett. 1984 McMullen BA, Fujikawa K. Amino acid sequence of the heavy chain of human alpha-factor XIIa (activated Hageman factor). J. Biol. Chem. 1985 Ikeo K, Takahashi K, Gojobori T. Evolutionary origin of numerous kringles in human and simian apolipoprotein(a). FEBS Lett. 1991 De Vos P, Schmitt J, Verhoeven G, Stunnenberg HG. Human androgen receptor expressed in HeLa cells activates transcription in vitro. Nucleic Acids Res. 1994 Schwabe JW, Teichmann SA. Nuclear receptors: the evolution of diversity. Sci. STKE 2004 Atkinson RA, Williams RJ. Solution structure of the kringle 4 domain from human plasminogen by 1H nuclear magnetic resonance spectroscopy and distance geometry. J. Mol. Biol. 1990 Castellino FJ, Beals JM. The genetic relationships between the kringle domains of human plasminogen, prothrombin, tissue plasminogen activator, urokinase, and coagulation factor XII. J. Mol. Evol. 1987 Nishikawa J, Kitaura M, Imagawa M, Nishihara T. Vitamin D receptor contains multiple dimerization interfaces that are functionally different. Nucleic Acids Res. 1995
Retinoid X receptor



The retinoic acid (retinoid X) receptor consists of 3 functional and structural domains: an N-terminal (modulatory) domain; a DNA binding domain that mediates specific binding to target DNA sequences (ligand-responsive elements); and a hormone binding domain. The N-terminal domain differs between retinoic acid isoforms; the small highly-conserved DNA-binding domain (~65 residues) occupies the central portion of the protein; and the ligand binding domain lies at the receptor C terminus.

Synonym(s): 2B nuclear receptor

Molecular Function DNA binding Molecular Function ligand-dependent nuclear receptor activity Molecular Function steroid binding Cellular Component nucleus Biological Process regulation of transcription, DNA-dependent Molecular Function zinc ion binding Nishikawa J, Kitaura M, Imagawa M, Nishihara T. Vitamin D receptor contains multiple dimerization interfaces that are functionally different. Nucleic Acids Res. 1995 De Vos P, Schmitt J, Verhoeven G, Stunnenberg HG. Human androgen receptor expressed in HeLa cells activates transcription in vitro. Nucleic Acids Res. 1994 Schwabe JW, Teichmann SA. Nuclear receptors: the evolution of diversity. Sci. STKE 2004
Helix-turn-helix, AraC type

Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' (HTH) motif. One major subfamily of these proteins [, ] is related to the arabinose operon regulatory protein AraC [], . Except for celD [], all of these proteins seem to be positive transcriptional factors.

Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The N-terminal and central regions of these proteins are presumed to interact with effector molecules and may be involved in dimerisation [].

The known structure of MarA () shows that the AraC domain is alpha helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27 angstroms, which causes the cognate DNA to bend.

Molecular Function transcription factor activity Cellular Component intracellular Biological Process regulation of transcription, DNA-dependent Molecular Function sequence-specific DNA binding Parker LL, Hall BG. Characterization and nucleotide sequence of the cryptic cel operon of Escherichia coli K12. Genetics 1990 Henikoff S, Wallace JC, Brown JP. Finding protein similarities with nucleotide sequence databases. Meth. Enzymol. 1990 Gallegos MT, Michan C, Ramos JL. The XylS/AraC family of regulators. Nucleic Acids Res. 1993 Bustos SA, Schleif RF. Functional domains of the AraC protein. Proc. Natl. Acad. Sci. U.S.A. 1993
Metallothionein, vertebrate

Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, ]. An empirical classification into three classes has been proposed by Fowler and coworkers [] and Kojima []. Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins, fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units [].



The members of family 1 are recognised by the sequence pattern K-x(1,2)-C-C-x-C-C-P-x(2)-C located at the beginning of the third exon. The taxonomic range of the members extends to vertebrates. Known characteristics: 60 to 68 AAs; 20 Cys (21 in one case), 19 of them are totally conserved; the protein sequence is divided into two structural domains, containing 9 and 11 Cys all binding 3 and 4 bivalent metal ions, respectively. The gene is composed of 3 exons, 2 introns and the splicing sites are conserved. Family 1 includes subfamilies: m1, m2, m3, m4, m, a, a1, a2, b, ba, t, all of them hit the same InterPro entry.

Molecular Function metal ion binding Kagi JH, Kojima Y. Chemistry and biochemistry of metallothionein. Experientia Suppl. 1987 Kagi JH. Overview of metallothionein. Meth. Enzymol. 1991 Kojima Y. Definitions and nomenclature of metallothioneins. Meth. Enzymol. 1991 Fowler BA, Hildebrand CE, Kojima Y, Webb M. Nomenclature of metallothionein. Experientia Suppl. 1987
Tubby, C-terminal



Kleyn PW, Fan W, Kovats SG, Lee JJ, Pulido JC, Wu Y, Berkemeier LR, Misumi DJ, Holmgren L, Charlat O, Woolf EA, Tayber O, Brody T, Shu P, Hawkins F, Kennedy B, Baldini L, Ebeling C, Alperin GD, Deeds J, Lakey ND, Culpepper J, Chen H, Glucksmann-Kuis MA, Carlson GA, Duyk GM, Moore KJ. Identification and characterization of the mouse obesity gene tubby: a member of a novel gene family. Cell 1996 Noben-Trauth K, Naggert JK, North MA, Nishina PM. A candidate gene for the mouse mutation tubby. Nature 1996 Boggon TJ, Shan WS, Santagata S, Myers SC, Shapiro L. Implication of tubby proteins as transcription factors by structure-based functional analysis. Science 1999 Carroll K, Gomez C, Shapiro L. Tubby proteins: the plot thickens. Nat. Rev. Mol. Cell Biol. 2004
C2 calcium-dependent membrane targeting The C2 domain is a Ca2+-dependent membrane-targeting module found in many cellular proteins involved in signal transduction or membrane trafficking. C2 domains are unique among membrane targeting domains in that they show wide range of lipid selectivity for the major components of cell membranes, including phosphatidylserine and phosphatidylcholine. This C2 domain is about 116 amino-acid residues and is located between the two copies of the C1 domain in Protein Kinase C (that bind phorbol esters and diacylglycerol) (see ) and the protein kinase catalytic domain (see ). Regions with significant homology [] to the C2-domain have been found in many proteins. The C2 domain is thought to be involved in calcium-dependent phospholipid binding [] and in membrane targetting processes such as subcellular localisation.

The 3D structure of the C2 domain of synaptotagmin has been reported [], the domain forms an eight-stranded beta sandwich constructed around a conserved 4-stranded motif, designated a C2 key []. Calcium binds in a cup-shaped depression formed by the N- and C-terminal loops of the C2-key motif. Structural analyses of several C2 domains have shown them to consist of similar ternary structures in which three Ca2+-binding loops are located at the end of an 8 stranded antiparallel beta sandwich.

Sutton RB, Davletov BA, Berghuis AM, Sudhof TC, Sprang SR. Structure of the first C2 domain of synaptotagmin I: a novel Ca2+/phospholipid-binding fold. Cell 1995 Davletov BA, Sudhof TC. A single C2 domain from synaptotagmin I is sufficient for high affinity Ca2+/phospholipid binding. J. Biol. Chem. 1993 Brose N, Hofmann K, Hata Y, Sudhof TC. Mammalian homologues of Caenorhabditis elegans unc-13 gene define novel family of C2-domain proteins. J. Biol. Chem. 1995
Protein phosphatase 2A, regulatory subunit PR55 Protein phosphatase 2A (PP2A) is a serine/threonine phosphatase implicated in many cellular processes, including the regulation of metabolic enzymes and proteins involved in signal transduction [, ]. PP2A is a trimer composed of a 36 kDa catalytic subunit, a 65 kDa regulatory subunit (subunit A) and a variable third subunit (subunit B) [, ].

One form of the third subunit is a 55 kDa protein (PR55), which exists in Drosophila melanogaster and yeast, and has up to three forms in mammals [, ]. PR55 may act as a substrate recognition unit, or may help to target the enzyme to the correct subcellular location [].

Cellular Component protein phosphatase type 2A complex Biological Process signal transduction Molecular Function protein phosphatase type 2A regulator activity Mayer RE, Hendrix P, Cron P, Matthies R, Stone SR, Goris J, Merlevede W, Hofsteenge J, Hemmings BA. Structure of the 55-kDa regulatory subunit of protein phosphatase 2A: evidence for a neuronal-specific isoform. Biochemistry 1991 Pallas DC, Weller W, Jaspers S, Miller TB, Lane WS, Roberts TM. The third subunit of protein phosphatase 2A (PP2A), a 55-kilodalton protein which is apparently substituted for by T antigens in complexes with the 36- and 63-kilodalton PP2A subunits, bears little resemblance to T antigens. J. Virol. 1992
Proteinase inhibitor I25, cystatin


The cystatins are cysteine proteinase inhibitors belonging to MEROPS inhibitor family I25, clan IH [, , ]. They mainly inhibit peptidases belonging to peptidase families C1 (papain family) and C13 (legumain family). The cystatin family includes:

  • The Type 3 cystatins, which are multidomain proteins. The mammalian representatives of this group are the kininogens. There are three different kininogens in mammals: H- (high molecular mass, ) and L- (low molecular mass) kininogen which are found in a number of species, and T-kininogen that is found only in rat.


Molecular Function cysteine-type endopeptidase inhibitor activity Turk V, Bode W. The cystatins: protein inhibitors of cysteine proteinases. FEBS Lett. 1991 Rawlings ND, Barrett AJ. Evolution of proteins of the cystatin superfamily. J. Mol. Evol. 1990 Abrahamson M, Alvarez-Fernandez M, Nathanson CM. Cystatins. Biochem. Soc. Symp. 2003
Ubiquitin-activating enzyme, E1-like

The post-translational attachment of ubiquitin () to proteins (ubiquitinylation) alters the function, location or trafficking of a protein, or targets it to the 26S proteasome for degradation [, , ]. Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1), a ubiquitin-conjugating enzyme (E2, ), and a ubiquitin ligase (E3, , ), which work sequentially in a cascade []. The E1 enzyme is responsible for activating ubiquitin, the first step in ubiquitinylation. The E1 enzyme hydrolyses ATP and adenylates the C-terminal glycine residue of ubiquitin, and then links this residue to the active site cysteine of E1, yielding a ubiquitin-thioester and free AMP. To be fully active, E1 must non-covalently bind to and adenylate a second ubiquitin molecule. The E1 enzyme can then transfer the thioester-linked ubiquitin molecule to a cysteine residue on the ubiquitin-conjugating enzyme, E2, in an ATP-dependent reaction.

Biological Process protein modification process Molecular Function small protein activating enzyme activity Burger AM, Seth AK. The ubiquitin-mediated protein degradation pathway in cancer: therapeutic implications. Eur. J. Cancer 2004 Passmore LA, Barford D. Getting into position: the catalytic mechanisms of protein ubiquitylation. Biochem. J. 2004 Pickart CM, Fushman D. Polyubiquitin chains: polymeric protein signals. 2004 Sun L, Chen ZJ. The novel functions of ubiquitination in signaling. Curr. Opin. Cell Biol. 2004
Retroviral VpR/VpX protein Human immunodeficiency virus (HIV) is the human retrovirus associated with AIDS (acquired immune deficiency syndrome), and SIV its simian counterpart. Three main groups of primate lentivirus are known, designated Human immunodeficiency virus 1 (HIV-1), Human immunodeficiency virus 2 (HIV-2)/Simian immunodeficiency virus - mac (SIVMAC)/Simian immunodeficiency virus - sm (SIVSM) and Simian immunodeficiency virus - agm (SIVAGM). Simian immunodeficiency virus - mnd (SIVMND) has been suggested to represent a fourth distinct group []. These groups are believed to have diverged from a common ancestor long before the spread of AIDS in humans. Genetic variation in HIV-1 and HIV-2 has been studied extensively, and the nucleotide sequences reported for several strains [].

ORF analysis has revealed two open reading frames, yielding the so-called R- and X-ORF proteins, whose functions are unknown, but which show a high degree of sequence similarity.

Hasegawa A, Tsujimoto H, Maki N, Ishikawa K, Miura T, Fukasawa M, Miki K, Hayami M. Genomic divergence of HIV-2 from Ghana. AIDS Res. Hum. Retroviruses 1989 Tsujimoto H, Hasegawa A, Maki N, Fukasawa M, Miura T, Speidel S, Cooper RW, Moriyama EN, Gojobori T, Hayami M. Sequence of a novel simian immunodeficiency virus from a wild-caught African mandrill. Nature 1989
Peptidase M7, snapalysin





This group of metallopeptidases belong to the MEROPS peptidase family M7 (snapalysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA.

With a molecular weight of around 16kDa, Streptomyces extracellular neutral protease is one of the smallest known proteases []; it is capable of hydrolysing milk proteins []. The enzyme is synthesised as a proenzyme with a signal peptide, a propeptide and an active domain that contains the conserved HEXXH motif characteristic of metalloproteases. Although family M7 shows active site sequence similarity to other members, it differs in one major respect: the third zinc ligand appears to be an aspartate residue rather than the usual histidine.

Molecular Function metalloendopeptidase activity Cellular Component extracellular region Biological Process proteolysis Molecular Function zinc ion binding Rawlings ND, Barrett AJ. Evolutionary families of metallopeptidases. Meth. Enzymol. 1995

PAS domains are involved in many signalling proteins where they are used as a signal sensor domain. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in:

  • Per- period circadian protein
  • Arnt- Ah receptor nuclear translocator protein
  • Sim- single-minded protein.
  • PAS domains are often associated with PAC domains . It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].

    Molecular Function signal transducer activity Biological Process signal transduction Zhulin IB, Taylor BL, Dixon R. PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox. Trends Biochem. Sci. 1997 Hefti MH, Francoijs KJ, de Vries SC, Dixon R, Vervoort J. The PAS fold. A redefinition of the PAS domain based upon structural prediction. Eur. J. Biochem. 2004 Amezcua CA, Harper SM, Rutter J, Gardner KH. Structure and interactions of PAS kinase N-terminal PAS domain: model for intramolecular kinase regulation. Structure 2002
    Fimbrial biogenesis outer membrane usher protein In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two- component assembly and transport system which is composed of a periplasmic chaperone (see ) and an outer membrane protein which has been termed a molecular 'usher' [, , ].

    The usher protein is rather large (from 86 to 100 Kd) and seems to be mainly composed of membrane-spanning beta-sheets, a structure reminiscent of porins. Although the degree of sequence similarity of these proteins is not very high they share a number of characteristics. One of these is the presence of two pairs of cysteines, the first one located in the N-terminal part and the second at the C-terminal extremity that are probably involved in disulphide bonds. The best conserved region is located in the central part of these proteins.

    Molecular Function transporter activity Biological Process transport Cellular Component membrane Schifferli DM, Alrutz MA. Permissive linker insertion sites in the outer membrane protein of 987P fimbriae of Escherichia coli. J. Bacteriol. 1994 Jacob-Dubuisson F, Striker R, Hultgren SJ. Chaperone-assisted self-assembly of pili independent of cellular energy. J. Biol. Chem. 1994 Van Rosmalen M, Saier MH Jr. Structural and evolutionary relationships between two families of bacterial extracytoplasmic chaperone proteins which function cooperatively in fimbrial assembly. Res. Microbiol. 1993
    P2Y4 purinoceptor

    G-protein-coupled receptors, GPCRs, constitute a vast protein family that encompasses a wide range of functions (including various autocrine, paracrine and endocrine processes). They show considerable diversity at the sequence level, on the basis of which they can be separated into distinct groups. We use the term clan to describe the GPCRs, as they embrace a group of families for which there are indications of evolutionary relationship, but between which there is no statistically significant similarity in sequence []. The currently known clan members include the rhodopsin-like GPCRs, the secretin-like GPCRs, the cAMP receptors, the fungal mating pheromone receptors, and the metabotropic glutamate receptor family. There is a specialised database for GPCRs (


    In addition to their role in energy metabolism, purines (especially adenosine and adenine nucleotides) produce a wide range of pharmacological effects mediated by activation of cell surface receptors []. ATP is a co-transmitter in sympathetic nerves in the autonomic nervous system, where it exerts an important physiological role in the regulation of smooth muscle activity, stimulating relaxation of intestinal smooth muscle and contraction of the bladder. Receptors for adenine nucleotides are involved in a number of other physiological pathways, including stimulation of platelet activation by ADP, which is released from the vascular endothelium following injury. ATP has excitatory effects in the CNS []. Distinct receptors exist for adenosine. The main effects of adenosine in the periphery include vasodilation, bronchoconstriction, immunosuppression, inhibition of platelet aggregation, cardiac depression, stimulation of nociceptive afferents, inhibition of neurotransmitter release, and inhibition of the release of hormones. In the CNS, adenosine exerts a pre- and post-synaptic depressant action, reducing motor activity, depressing respiration, inducing sleep and relieving anxiety. The physiological role of adenosine is believed to be to adjust energy demands in line with oxygen supply [].

    Purinoceptors have been classified as P1 or P2, depending on their preference for adenosine or adenine nucleotides respectively. Adenosine receptors (P1 purinoceptors) are characterised by their affinity for adenosine and by the ability of methylxanthines to act as antagonists []. Adenosine has very low affinity for P2 purinoceptors.

    The P2Y receptor is found in smooth muscle (e.g., taeni caeci) and in vascular tissue, where it induces vasodilation through endothelium-dependent release of nitric oxide. The receptor activates phosphoinositide metabolism through a pertussis-toxin-insensitive G-protein, probably belonging to the Gi/Go class [].

    A new subtype of P2 purinoceptors has been isolated []. Its deduced amino acid sequence is consistent with a GPCR that is 51% identical to the human P2Y2 receptor and 35% identical to the chicken P2Y1 receptor []. P2Y4 is expressed in the placenta, with low levels in the lung and vascular smoothmuscle. In cells stably expressing the receptor, UTP and UDP have been shown to stimulate the formation of inositol phosphates with equivalent potency and maximal effect, while ATP behaves as a partial agonist, and ADP is almost inactive []. The receptor is thus a new member of the P2 purinergic receptor family that functionally behaves as a pyrimidinergic receptor []. P2Y4 can couple to both Gi and Gq proteins to activate phospholipase C [].

    Biological Process G-protein coupled receptor protein signaling pathway Cellular Component integral to membrane Molecular Function purinergic nucleotide receptor activity, G-protein coupled Birnbaumer L. G proteins in signal transduction. Annu. Rev. Pharmacol. Toxicol. 1990 Casey PJ, Gilman AG. G protein involvement in receptor-effector coupling. J. Biol. Chem. 1988 Communi D, Pirotton S, Parmentier M, Boeynaems JM. Cloning and functional expression of a human uridine nucleotide receptor. J. Biol. Chem. 1995 Attwood TK, Findlay JB. Design of a discriminating fingerprint for G-protein-coupled receptors. Protein Eng. 1993 Communi D, Janssens R, Suarez-Huerta N, Robaye B, Boeynaems JM. Advances in signalling by extracellular nucleotides. the role and transduction mechanisms of P2Y receptors. Cell. Signal. 2000 Attwood TK, Findlay JB. Fingerprinting G-protein-coupled receptors. Protein Eng. 1994 Watson S, Arkinstall S. Adenosine and adenine nucleotides. ISBN:0127384405 1994

    Complement components C3, C4 and C5 are large glycoproteins that have important functions in the immune response and host defence []. They have a wide variety of biological activities and are proteolytically activated by cleavage at a specific site, forming a- and b-fragments []. A-fragments form distinct structural domains of approximately 76 amino acids, coded for by a single exon within the complement protein gene. The C3a, C4a and C5a components are referred to as anaphylatoxins [, ]: they cause smooth muscle contraction, histamine release from mast cells, and enhanced vascular permeability []. They also mediate chemotaxis, inflammation, and generation of cytotoxic oxygen radicals []. The proteins are highly hydrophilic, with a mainly alpha-helical structure held together by 3 disulphide bridges [].

    Fibulins are secreted glycoproteins that become incorporated into a fibrillar extracellular matrix when expressed by cultured cells or added exogenously to cell monolayers [, ]. The five known members of the family share an elongated structure and many calcium-binding sites, owing to the presence of tandem arrays of epidermal growth factor-like domains. They have overlapping binding sites for several basement-membrane proteins, tropoelastin, fibrillin, fibronectin and proteoglycans, and they participate in diverse supramolecular structures. The amino-terminal domain I of fibulin consists of three anaphylatoxin-like (AT) modules, each approximately 40 residues long and containing four or six cysteines. The structure of an AT module was determined for the complement-derived anaphylatoxin C3a, and was found to be a compact alpha-helical fold that is stabilised by three disulphide bridges in the pattern Cys1-4, Cys2-5 and Cys3-6 (where Cys is cysteine). The bulk of the remaining portion of the fibulin molecule is a series of nine EGF-like repeats [].

    Cellular Component extracellular region Gennaro R, Simonic T, Negri A, Mottola C, Secchi C, Ronchi S, Romeo D. C5a fragment of bovine complement. Purification, bioassays, amino-acid sequence and other structural studies. Eur. J. Biochem. 1986 Ogata RT, Rosa PA, Zepf NE. Sequence of the gene for murine complement component C4. J. Biol. Chem. 1989 Argraves WS, Tran H, Burgess WH, Dickerson K. Fibulin is an extracellular matrix and plasma glycoprotein with repeated domain structure. J. Cell Biol. 1990 Timpl R, Sasaki T, Kostka G, Chu ML. Fibulins: a versatile family of extracellular matrix proteins. Nat. Rev. Mol. Cell Biol. 2003 Pan TC, Sasaki T, Zhang RZ, Fassler R, Timpl R, Chu ML. Structure and expression of fibulin-2, a novel extracellular matrix protein with multiple EGF-like repeats and consensus motifs for calcium binding. J. Cell Biol. 1993 Fritzinger DC, Petrella EC, Connelly MB, Bredehorst R, Vogel CW. Primary structure of cobra complement component C3. J. Immunol. 1992
    Hok/gef cell toxic protein The hok/gef family of Gram-negative bacterial proteins are toxic to cells when over-expressed, killing the cells from within by interfering with a vital function in the cell membrane []. Some family members (flm) increase the stability of unstable RNA [], some (pnd) induce the degradation of stable RNA at higher than optimum growth temperatures [], while others affect the release of cellular magnesium by membrane alterations []. The proteins are short (50-70 residues), consisting of an N-terminal hydrophobic (possibly membrane spanning) domain, and a C-terminal periplasmic region, which contains the toxic domain. The C-terminal region contains a conserved cysteine residue that mediates homo-dimerisation in the gef protein, although dimerisation is not necessary for the toxic effect []. Cellular Component membrane Sakikawa T, Akimoto S, Ohnishi Y. The pnd gene in E. coli plasmid R16: nucleotide sequence and gene expression leading to cell Mg2+ release and stable RNA degradation. Biochim. Biophys. Acta 1989 Golub EI, Panzer HA. The F factor of Escherichia coli carries a locus of stable plasmid inheritance stm, similar to the parB locus of plasmid RI. Mol. Gen. Genet. 1988 Poulsen LK, Refn A, Molin S, Andersson P. Topographic analysis of the toxic Gef protein from Escherichia coli. Mol. Microbiol. 1991 Carboxyl transferase

    Members in this domain include biotin dependent carboxylases [, ]. The carboxyl transferase domain carries out the following reaction; transcarboxylation from biotin to an acceptor molecule. There are two recognised types of carboxyl transferase. One of them uses acyl-CoA and the other uses 2-oxo acid as the acceptor molecule of carbon dioxide. All of the members in this family utilise acyl-CoA as the acceptor molecule.

    Molecular Function ligase activity Toh H, Kondo H, Tanabe T. Molecular evolution of biotin-dependent carboxylases. Eur. J. Biochem. 1993 Thornton CG, Kumar GK, Haase FC, Phillips NF, Woo SB, Park VM, Magner WJ, Shenoy BC, Wood HG, Samols D. Primary structure of the monomer of the 12S subunit of transcarboxylase as deduced from DNA and characterization of the product expressed in Escherichia coli. J. Bacteriol. 1993
    Phosphofructokinase The enzyme-catalysed transfer of a phosphoryl group from ATP is an important reaction in a wide variety of biological processes []. One enzyme that utilises this reaction is phosphofructokinase (PFK), which catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6- bisphosphate, a key regulatory step in the glycolytic pathway [, ]. PFK exists as a homotetramer in bacteria and mammals (where each monomer possesses 2 similar domains), and as an octomer in yeast (where there are 4 alpha- (PFK1) and 4 beta-chains (PFK2), the latter, like the mammalian monomers, possessing 2 similar domains []).

    PFK is ~300 amino acids in length, and structural studies of the bacterial enzyme have shown it comprises two similar (alpha/beta) lobes: one involved in ATP binding and the other housing both the substrate-binding site and the allosteric site (a regulatory binding site distinct from the active site, but that affects enzyme activity). The identical tetramer subunits adopt 2 different conformations: in a 'closed' state, the bound magnesium ion bridges the phosphoryl groups of the enzyme products (ADP and fructose-1,6- bisphosphate); and in an 'open' state, the magnesium ion binds only the ADP [], as the 2 products are now further apart. These conformations are thought to be successive stages of a reaction pathway that requires subunit closure to bring the 2 molecules sufficiently close to react [].

    Deficiency in PFK leads to glycogenosis type VII (Tauri's disease), an autosomal recessive disorder characterised by severe nausea, vomiting, muscle cramps and myoglobinuria in response to bursts of intense or vigorous exercise []. Sufferers are usually able to lead a reasonably ordinary life by learning to adjust activity levels [].

    Molecular Function 6-phosphofructokinase activity Cellular Component 6-phosphofructokinase complex Biological Process glycolysis Raben N, Exelbert R, Spiegel R, Sherman JB, Nakajima H, Plotz P, Heinisch J. Functional expression of human mutant phosphofructokinase in yeast: genetic defects in French Canadian and Swiss patients with phosphofructokinase deficiency. Am. J. Hum. Genet. 1995 Shirakihara Y, Evans PR. Crystal structure of the complex of phosphofructokinase from Escherichia coli with its reaction products. J. Mol. Biol. 1988 Hellinga HW, Evans PR. Mutations in the active site of Escherichia coli phosphofructokinase. Nature 1987 Wegener G, Krause U. Different modes of activating phosphofructokinase, a key regulatory enzyme of glycolysis, in working vertebrate muscle. Biochem. Soc. Trans. 2002
    Frizzled cysteine-rich domain The Frizzled CRD (cysteine rich domain) is conserved in diverse proteins including several receptor tyrosine kinases [, , ]. In Drosophila melanogaster, members of the Frizzled family of tissue-polarity genes encode proteins that appear to function as cell-surface receptors for Wnts. The Frizzled genes belong to the seven transmembrane class of receptors (7TMR) and have in their extracellular region a cysteine-rich domain that has been implicated as the Wnt binding domain. Sequence similarity between the cysteine-rich domain of Frizzled and several receptor tyrosine kinases, which have roles in development, include the muscle-specific receptor tyrosine kinase (MuSK), the neuronal specific kinase (NSK2), and ROR1 and ROR2. The structure of this domain is known and is composed mainly of alpha helices. This domain contains ten conserved cysteines that form five disulphide bridges. Xu YK, Nusse R. The Frizzled CRD domain is conserved in diverse proteins including several receptor tyrosine kinases. Curr. Biol. 1998 Saldanha J, Singh J, Mahadevan D. Identification of a Frizzled-like cysteine rich domain in the extracellular region of developmental receptor tyrosine kinases. Protein Sci. 1998 Rehn M, Pihlajaniemi T, Hofmann K, Bucher P. The frizzled motif: in how many different protein families does it occur? Trends Biochem. Sci. 1998 Alkylbase DNA glycosidase, conserved site

    Alkylbase DNA glycosidases [] are DNA repair enzymes that hydrolyse the deoxyribose N-glycosidic bond to excise various alkylated bases from a damaged DNA polymer. In Escherichia coli there are two alkylbase DNA glycosidases: one (gene tag) which is constitutively expressed and which is specific for the removal of 3-methyladenine (), and one (gene alkA) which is induced during adaptation to alkylation and which can remove a variety of alkylation products (). Tag and alkA do not share any region of sequence similarity. In yeast there is an alkylbase DNA glycosidase (gene MAG1) [, ], which can remove 3-methyladenine or 7-methyladenine and which is structurally related to alkA. MAG and alkA are both proteins of about 300 amino acid residues. While the C- and N-terminal ends appear to be unrelated, there is a central region of about 130 residues which is well conserved.

    Molecular Function alkylbase DNA N-glycosylase activity Biological Process DNA repair Lindahl T, Sedgwick B, Sekiguchi M, Nakabeppu Y. Regulation and expression of the adaptive response to alkylating agents. Annu. Rev. Biochem. 1988 Berdal KG, Bjoras M, Bjelland S, Seeberg E. Cloning and expression in Escherichia coli of a gene for an alkylbase DNA glycosylase from Saccharomyces cerevisiae; a homologue to the bacterial alkA gene. EMBO J. 1990 Chen J, Derfler B, Samson L. Saccharomyces cerevisiae 3-methyladenine DNA glycosylase has homology to the AlkA glycosylase of E. coli and is induced in response to DNA alkylation damage. EMBO J. 1990