PDBsum entry: 1ggt

Blood coagulation

PDB-id

1ggt

	Biological unit* = asymmetric unit, as shown (as deduced by PQS*)


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PDB id:

1ggt

Name:

Blood coagulation

Title:

Three-dimensional structure of a transglutaminase: human blood coagulation factor xiii

Structure:

Coagulation factor xiii. Chain: a, b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Organ: blood

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: P00488 (F13A_HUMAN)

Seq:

Struc:

Seq:

Struc:

Seq:

732 a.a.

Struc:

710 a.a.*

Key:		PfamA domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme class:

E.C.2.3.2.13 [IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Protein glutamine + alkylamine = protein N₅-alkylglutamine + NH₃ (see diagram below)

Cofactor:

Calcium

Resolution:

2.65Å

R-factor:

0.216

Authors:

V.C.Yee,L.C.Pedersen,I.L.Trong,P.D.Bishop,R.E.Stenkamp, D.C.Teller

Key ref:

V.C.Yee et al. (1994). Three-dimensional structure of a transglutaminase: human blood coagulation factor XIII.. Proc Natl Acad Sci U S A, 91, 7296-7300. [PubMed id: 7913750] [DOI: 10.1073/pnas.91.15.7296]

Date:

25-Jan-94

Release date:

31-Jul-95

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Surface

Enzyme reaction for E.C.2.3.2.13

Protein glutamine	+	alkylamine	=	protein N(5)-alkylglutamine	+	NH(3)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

Key reference

DOI no: 10.1073/pnas.91.15.7296 Proc Natl Acad Sci U S A 91:7296-7300 (1994)

PubMed id: 7913750

Three-dimensional structure of a transglutaminase: human blood coagulation factor XIII.

V.C.Yee, L.C.Pedersen, I.Le Trong, P.D.Bishop, R.E.Stenkamp, D.C.Teller.

ABSTRACT

Mechanical stability in many biological materials is provided by the crosslinking of large structural proteins with gamma-glutamyl-epsilon-lysyl amide bonds. The three-dimensional structure of human recombinant factor XIII (EC 2.3.2.13 zymogen; protein-glutamine:amine gamma-glutamyltransferase a chain), a transglutaminase zymogen, has been solved at 2.8-A resolution by x-ray crystallography. This structure shows that each chain of the homodimeric protein is folded into four sequential domains. A catalytic triad reminiscent of that observed in cysteine proteases has been identified in the core domain. The amino-terminal activation peptide of each subunit crosses the dimer interface and partially occludes the opening of the catalytic cavity in the second subunit, preventing substrate binding to the zymogen. A proposal for the mechanism of activation by thrombin and calcium is made that details the structural events leading to active factor XIIIa'.

Literature references that cite this PDB file's key reference

PubMed id Reference

19805099 C.Ottmann, R.Rose, F.Huttenlocher, A.Cedzich, P.Hauske, M.Kaiser, R.Huber, and A.Schaller (2009).
Structural basis for Ca2+-independence and activation by homodimerization of tomato subtilase 3.

Proc Natl Acad Sci U S A, 106, 17223-17228.

PDB codes: 3i6s 3i74

19438481 R.Anwar, and S.Langlois (2009).
The Arg703Trp missense mutation in F13A1 is a de novo event.

Br J Haematol, 146, 118-120.

19850674 U.Tagami, N.Shimba, M.Nakamura, K.Yokoyama, E.Suzuki, and T.Hirokawa (2009).
Substrate specificity of microbial transglutaminase as revealed by three-dimensional docking simulation and mutagenesis.

Protein Eng Des Sel, 22, 747-752.

17965157 A.B.Hervás, I.Canosa, and E.Santero (2008).
Transcriptome analysis of Pseudomonas putida in response to nitrogen availability.

J Bacteriol, 190, 416-420.

18275437 C.H.Trinh, W.Sh Elsayed, P.Eshghi, E.Miri-Moghaddam, A.Zadeh-Vakili, A.F.Markham, and R.Anwar (2008).
Molecular analysis of sixteen unrelated factor XIIIA deficient families from south-east of Iran.

Br J Haematol, 140, 581-584.

18092889 D.M.Pinkas, P.Strop, A.T.Brunger, and C.Khosla (2007).
Transglutaminase 2 undergoes a large conformational change upon activation.

PLoS Biol, 5, e327.

PDB code: 2q3z

17653193 P.D.Fortin, C.T.Walsh, and N.A.Magarvey (2007).
A transglutaminase homologue as a condensation catalyst in antibiotic assembly lines.

Nature, 448, 824-827.

17479223 P.K.Carvajal-Vallejos, A.Campos, P.Fuentes-Prior, E.Villalobos, A.M.Almeida, E.Barberà, J.M.Torné, and M.Santos (2007).
Purification and in vitro refolding of maize chloroplast transglutaminase over-expressed in Escherichia coli.

Biotechnol Lett, 29, 1255-1262.

17880458 V.Ivaskevicius, J.Windyga, B.Baran, V.Schroeder, J.Junen, K.Bykowska, E.Seifried, H.P.Kohler, and J.Oldenburg (2007).
Phenotype-genotype correlation in eight Polish patients with inherited Factor XIII deficiency: identification of three novel mutations.

Haemophilia, 13, 649-657.

16479194 A.Vysokovsky, N.Rosenberg, R.Dardik, U.Seligsohn, and A.Inbal (2006).
Effect of four missense mutations in the factor XIII A-subunit gene on protein stability: studies with recombinant proteins.

Blood Coagul Fibrinolysis, 17, 125-130.

17179049 G.E.Begg, L.Carrington, P.H.Stokes, J.M.Matthews, M.A.Wouters, A.Husain, L.Lorand, S.E.Iismaa, and R.M.Graham (2006).
Mechanism of allosteric regulation of transglutaminase 2 by GTP.

Proc Natl Acad Sci U S A, 103, 19683-19688.

16988554 M.Kusch, C.Grundmann, S.Keitel, R.Seitz, and H.König (2006).
A novel assay for factor XIII based on cross-linking of synthetic peptides: analysis of different substrates.

Blood Coagul Fibrinolysis, 17, 575-580.

16409483 S.Wu, Z.Wang, N.Dong, X.Bai, and C.Ruan (2006).
A novel compound heterozygous mutation in the F13A gene causing hereditary factor XIII deficiency in a Chinese family.

J Thromb Haemost, 4, 267-269.

15964983 J.H.Lee, J.M.Choi, C.Lee, K.J.Yi, and Y.Cho (2005).
Structure of a peptide:N-glycanase-Rad23 complex: insight into the deglycosylation for denatured glycoproteins.

Proc Natl Acad Sci U S A, 102, 9144-9149.

PDB codes: 1x3w 1x3z

16241947 N.Komanasin, A.J.Catto, T.S.Futers, A.van Hylckama Vlieg, F.R.Rosendaal, and R.A.Ariëns (2005).
A novel polymorphism in the factor XIII B-subunit (His95Arg): relationship to subunit dissociation and venous thrombosis.

J Thromb Haemost, 3, 2487-2496.

16155204 S.Singh, C.C.Cornilescu, R.C.Tyler, G.Cornilescu, M.Tonelli, M.S.Lee, and J.L.Markley (2005).
Solution structure of a late embryogenesis abundant protein (LEA14) from Arabidopsis thaliana, a cellular stress-related protein.

Protein Sci, 14, 2601-2609.

PDB code: 1xo8

16128900 W.Onland, A.N.Böing, A.B.Meijer, M.C.Schaap, R.Nieuwland, K.Haasnoot, A.Sturk, and M.Peters (2005).
Congenital deficiency of factor XIII caused by two missense mutations in a Dutch family.

Haemophilia, 11, 539-547.

15456491 A.Vysokovsky, R.Saxena, M.Landau, A.Zivelin, R.Eskaraev, N.Rosenberg, U.Seligsohn, and A.Inbal (2004).
Seven novel mutations in the factor XIII A-subunit gene causing hereditary factor XIII deficiency in 10 unrelated families.

J Thromb Haemost, 2, 1790-1797.

15010546 R.A.Chica, P.Gagnon, J.W.Keillor, and J.N.Pelletier (2004).
Tissue transglutaminase acylation: Proposed role of conserved active site Tyr and Trp residues revealed by molecular modeling of peptide substrate binding.

Protein Sci, 13, 979-991.

15112292 T.Takazawa, N.Kamiya, H.Ueda, and T.Nagamune (2004).
Enzymatic labeling of a single chain variable fragment of an antibody with alkaline phosphatase by microbial transglutaminase.

Biotechnol Bioeng, 86, 399-404.

12535215 A.Kon, H.Takeda, H.Sasaki, K.Yoneda, K.Nomura, B.Ahvazi, P.M.Steinert, K.Hanada, and I.Hashimoto (2003).
Novel transglutaminase 1 gene mutations (R348X/Y365D) in a Japanese family with lamellar ichthyosis.

J Invest Dermatol, 120, 170-172.

14604285 B.Duan, X.Wang, H.Chu, Y.Hu, X.Huang, B.Qu, H.Wang, and Z.Wang (2003).
Deficiency of factor XIII gene in Chinese: 3 novel mutations.

Int J Hematol, 78, 251-255.

12606569 C.Hirsch, D.Blom, and H.L.Ploegh (2003).
A role for N-glycanase in the cytosolic turnover of glycoproteins.

EMBO J, 22, 1036-1046.

12801297 E.Birben, C.Oner, R.Oner, C.Altay, and A.Gürgey (2003).
Identification of an inframe deletion and a missense mutation in the factor XIIIA gene in two Turkish patients.

Eur J Haematol, 71, 39-43.

12563291 L.Lorand, and R.M.Graham (2003).
Transglutaminases: crosslinking enzymes with pleiotropic functions.

Nat Rev Mol Cell Biol, 4, 140-156.

12534611 M.Akiyama, Y.Takizawa, Y.Suzuki, and H.Shimizu (2003).
A novel homozygous mutation 371delA in TGM1 leads to a classic lamellar ichthyosis phenotype.

Br J Dermatol, 148, 149-153.

12542526 M.Raghunath, H.C.Hennies, B.Ahvazi, M.Vogel, A.Reis, P.M.Steinert, and H.Traupe (2003).
Self-healing collodion baby: a dynamic phenotype explained by a particular transglutaminase-1 mutation.

J Invest Dermatol, 120, 224-228.

12621151 P.M.Quigley, K.Korotkov, F.Baneyx, and W.G.Hol (2003).
The 1.6-A crystal structure of the class of chaperones represented by Escherichia coli Hsp31 reveals a putative catalytic triad.

Proc Natl Acad Sci U S A, 100, 3137-3142.

PDB code: 1n57

14566064 S.E.Iismaa, S.Holman, M.A.Wouters, L.Lorand, R.M.Graham, and A.Husain (2003).
Evolutionary specialization of a tryptophan indole group for transition-state stabilization by eukaryotic transglutaminases.

Proc Natl Acad Sci U S A, 100, 12636-12641.

11980702 B.Ahvazi, H.C.Kim, S.H.Kee, Z.Nemes, and P.M.Steinert (2002).
Three-dimensional structure of the human transglutaminase 3 enzyme: binding of calcium ions changes structure for activation.

EMBO J, 21, 2055-2067.

PDB codes: 1l9m 1l9n

12392549 D.Sblattero, F.Florian, E.Azzoni, T.Zyla, M.Park, V.Baldas, T.Not, A.Ventura, A.Bradbury, and R.Marzari (2002).
The analysis of the fine specificity of celiac disease antibodies using tissue transglutaminase fragments.

Eur J Biochem, 269, 5175-5181.

12162574 H.Okudo, M.Kito, T.Moriyama, T.Ogawa, and R.Urade (2002).
Transglutaminase activity of human ER-60.

Biosci Biotechnol Biochem, 66, 1423-1426.

11867708 S.Liu, R.A.Cerione, and J.Clardy (2002).
Structural basis for the guanine nucleotide-binding activity of tissue transglutaminase and its regulation of transamidation activity.

Proc Natl Acad Sci U S A, 99, 2743-2747.

PDB code: 1kv3

11867764 S.N.Murthy, S.Iismaa, G.Begg, D.M.Freymann, R.M.Graham, and L.Lorand (2002).
Conserved tryptophan in the core domain of transglutaminase is essential for catalytic activity.

Proc Natl Acad Sci U S A, 99, 2738-2742.

11329258 E.Ballestar, M.Boix-Chornet, and L.Franco (2001).
Conformational changes in the nucleosome followed by the selective accessibility of histone glutamines in the transglutaminase reaction: effects of ionic strength.

Biochemistry, 40, 1922-1929.

11251583 M.Akiyama, Y.Takizawa, T.Kokaji, and H.Shimizu (2001).
Novel mutations of TGM1 in a child with congenital ichthyosiform erythroderma.

Br J Dermatol, 144, 401-407.

11407995 M.Akiyama, Y.Takizawa, Y.Suzuki, A.Ishiko, I.Matsuo, and H.Shimizu (2001).
Compound heterozygous TGM1 mutations including a novel missense mutation L204Q in a mild form of lamellar ichthyosis.

J Invest Dermatol, 116, 992-995.

11168522 R.Anwar, L.Gallivan, C.Trinh, F.Hill, and A.Markham (2001).
Identification of a new Leu354Pro mutation responsible for factor XIII deficiency.

Eur J Haematol, 66, 133-136.

10886517 B.A.Jessen, M.A.Phillips, A.Hovnanian, and R.H.Rice (2000).
Role of Sp1 response element in transcription of the human transglutaminase 1 gene.

J Invest Dermatol, 115, 113-117.

10684262 S.S.Akimov, D.Krylov, L.F.Fleischman, and A.M.Belkin (2000).
Tissue transglutaminase is an integrin-binding adhesion coreceptor for fibronectin.

J Cell Biol, 148, 825-838.

10561600 C.M.Bergamini, M.Dean, G.Matteucci, S.Hanau, F.Tanfani, C.Ferrari, M.Boggian, and A.Scatturin (1999).
Conformational stability of human erythrocyte transglutaminase. Patterns of thermal unfolding at acid and alkaline pH.

Eur J Biochem, 266, 575-582.

10452618 K.S.Makarova, L.Aravind, and E.V.Koonin (1999).
A superfamily of archaeal, bacterial, and eukaryotic proteins homologous to animal transglutaminases.

Protein Sci, 8, 1714-1719.

10531483 M.S.Weiss, and R.Hilgenfeld (1999).
Dehydration leads to a phase transition in monoclinic factor XIII crystals.

Acta Crystallogr D Biol Crystallogr, 55, 1858-1862.

10479736 M.S.Weiss, and R.Hilgenfeld (1999).
A method to detect nonproline cis peptide bonds in proteins.

Biopolymers, 50, 536-544.

10411627 R.Casadio, E.Polverini, P.Mariani, F.Spinozzi, F.Carsughi, A.Fontana, P.Polverino de Laureto, G.Matteucci, and C.M.Bergamini (1999).
The structural basis for the regulation of tissue transglutaminase by calcium ions.

Eur J Biochem, 262, 672-679.

PDB code: 1fau

9545389 H.C.Hennies, W.Küster, V.Wiebe, A.Krebsová, and A.Reis (1998).
Genotype/phenotype correlation in autosomal recessive lamellar ichthyosis.

Am J Hum Genet, 62, 1052-1061.

9692205 K.Yokoyama, Y.Kikuchi, and H.Yasueda (1998).
Overproduction of DnaJ in Escherichia coli improves in vivo solubility of the recombinant fish-derived transglutaminase.

Biosci Biotechnol Biochem, 62, 1205-1210.

9326318 E.Laiho, J.Ignatius, H.Mikkola, V.C.Yee, D.C.Teller, K.M.Niemi, U.Saarialho-Kere, J.Kere, and A.Palotie (1997).
Transglutaminase 1 mutations in autosomal recessive congenital ichthyosis: private and recurrent mutations in an isolated population.

Am J Hum Genet, 61, 529-538.

9144031 J.W.van Wersch, M.E.Vooijs, and J.M.Ubachs (1997).
Coagulation factor XIII in pregnant smokers and non-smokers.

Int J Clin Lab Res, 27, 68-71.

9033388 K.B.Lewis, D.C.Teller, J.Fry, G.W.Lasser, and P.D.Bishop (1997).
Crosslinking kinetics of the human transglutaminase, factor XIII[A2], acting on fibrin gels and gamma-chain peptides.

Biochemistry, 36, 995.

9305955 S.E.Iismaa, L.Chung, M.J.Wu, D.C.Teller, V.C.Yee, and R.M.Graham (1997).
The core domain of the tissue transglutaminase Gh hydrolyzes GTP and ATP.

Biochemistry, 36, 11655-11664.

8548458 J.J.Tesmer, T.J.Klem, M.L.Deras, V.J.Davisson, and J.L.Smith (1996).
The crystal structure of GMP synthetase reveals a novel catalytic triad and is a structural paradigm for two enzyme families.

Nat Struct Biol, 3, 74-86.

PDB code: 1gpm

8892731 S.Aslam, D.J.Bowen, T.Mandalaki, R.Gialeraki, and G.R.Standen (1996).
Factor XIII(A) subunit deficiency due to a homozygous 13-base pair deletion in exon 3 of the A subunit gene.

Am J Hematol, 53, 77-80.

7556189 H.Yasueda, K.Nakanishi, Y.Kumazawa, K.Nagase, M.Motoki, and H.Matsui (1995).
Tissue-type transglutaminase from red sea bream (Pagrus major). Sequence analysis of the cDNA and functional expression in Escherichia coli.

Eur J Biochem, 232, 411-419.

7773290 L.J.Russell, J.J.DiGiovanna, G.R.Rogers, P.M.Steinert, N.Hashem, J.G.Compton, and S.J.Bale (1995).
Mutations in the gene for transglutaminase 1 in autosomal recessive lamellar ichthyosis.

Nat Genet, 9, 279-283.

8555083 R.Anwar, A.D.Stewart, K.J.Miloszewski, M.S.Losowsky, and A.F.Markham (1995).
Molecular basis of inherited factor XIII deficiency: identification of multiple mutations provides insights into protein function.

Br J Haematol, 91, 728-735.

8547093 S.Aslam, M.C.Poon, V.C.Yee, D.J.Bowen, and G.R.Standen (1995).
Factor XIIIA Calgary: a candidate missense mutation (Leu667Pro) in the beta barrel 2 domain of the factor XIIIA subunit.

Br J Haematol, 91, 452-457.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.