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Blood coagulation
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PDB id
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1ggt
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.2.3.2.13
- Protein-glutamine gamma-glutamyltransferase.
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Reaction:
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Protein glutamine + alkylamine = protein N5-alkylglutamine + NH3
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Protein glutamine
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+
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alkylamine
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=
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protein N(5)-alkylglutamine
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+
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NH(3)
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Cofactor:
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Calcium
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Cellular component
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extracellular region
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3 terms
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Biological process
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wound healing
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5 terms
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Biochemical function
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transferase activity
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4 terms
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DOI no:
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Proc Natl Acad Sci U S A
91:7296-7300
(1994)
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PubMed id:
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Three-dimensional structure of a transglutaminase: human blood coagulation factor XIII.
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V.C.Yee,
L.C.Pedersen,
I.Le Trong,
P.D.Bishop,
R.E.Stenkamp,
D.C.Teller.
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ABSTRACT
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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'.
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Literature references that cite this PDB file's key reference
|
|
 |
| |
PubMed id
|
 |
Reference
|
 |
|
|
|
 |
I.Komáromi,
Z.Bagoly,
and
L.Muszbek
(2011).
Factor XIII: novel structural and functional aspects.
|
| |
J Thromb Haemost, 9,
9.
|
 |
|
|
|
|
 |
Q.Li,
X.Li,
C.Li,
L.Chen,
J.Song,
Y.Tang,
and
X.Xu
(2011).
A network-based multi-target computational estimation scheme for anticoagulant activities of compounds.
|
| |
PLoS One, 6,
e14774.
|
 |
|
|
|
|
 |
E.Ortner,
V.Schroeder,
R.Walser,
O.Zerbe,
and
H.P.Kohler
(2010).
Sensitive and selective detection of free FXIII activation peptide: a potential marker of acute thrombotic events.
|
| |
Blood, 115,
5089-5096.
|
 |
|
|
|
|
 |
H.Kumeta,
N.Miwa,
K.Ogura,
Y.Kai,
T.Mizukoshi,
N.Shimba,
E.Suzuki,
and
F.Inagaki
(2010).
The NMR structure of protein-glutaminase from Chryseobacterium proteolyticum.
|
| |
J Biomol NMR, 46,
251-255.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
L.Tei,
G.Mazooz,
Y.Shellef,
R.Avni,
K.Vandoorne,
A.Barge,
V.Kalchenko,
M.W.Dewhirst,
L.Chaabane,
L.Miragoli,
D.Longo,
M.Neeman,
and
S.Aime
(2010).
Novel MRI and fluorescent probes responsive to the Factor XIII transglutaminase activity.
|
| |
Contrast Media Mol Imaging, 5,
213-222.
|
 |
|
|
|
|
 |
M.Akiyama,
K.Sakai,
T.Yanagi,
S.Fukushima,
H.Ihn,
K.Hitomi,
and
H.Shimizu
(2010).
Transglutaminase1 preferred substrate peptide K5 is an efficient tool in diagnosis of lamellar ichthyosis.
|
| |
Am J Pathol, 176,
1592-1599.
|
 |
|
|
|
|
 |
N.Louhichi,
M.Medhaffar,
I.Hadjsalem,
E.Mkaouar-Rebai,
N.Fendri-Kriaa,
H.Kanoun,
F.Yaïch,
T.Souissi,
M.Elloumi,
and
F.Fakhfakh
(2010).
Congenital factor XIII deficiency caused by two mutations in eight Tunisian families: molecular confirmation of a founder effect.
|
| |
Ann Hematol, 89,
499-504.
|
 |
|
|
|
|
 |
S.Maerz,
Y.Funakoshi,
Y.Negishi,
T.Suzuki,
and
S.Seiler
(2010).
The Neurospora peptide:N-glycanase ortholog PNG1 is essential for cell polarity despite its lack of enzymatic activity.
|
| |
J Biol Chem, 285,
2326-2332.
|
 |
|
|
|
|
 |
V.Ivaskevicius,
A.Biswas,
C.Bevans,
V.Schroeder,
H.P.Kohler,
H.Rott,
S.Halimeh,
P.E.Petrides,
H.Lenk,
M.Krause,
B.Miterski,
U.Harbrecht,
and
J.Oldenburg
(2010).
Identification of eight novel coagulation factor XIII subunit A mutations: implied consequences for structure and function.
|
| |
Haematologica, 95,
956-962.
|
 |
|
|
|
|
 |
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:
|
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|
|
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|
 |
M.D.Andersen,
M.Kjalke,
S.Bang,
I.Lautrup-Larsen,
P.Becker,
A.S.Andersen,
O.H.Olsen,
and
H.R.Stennicke
(2009).
Coagulation factor XIII variants with altered thrombin activation rates.
|
| |
Biol Chem, 390,
1279-1283.
|
 |
|
|
|
|
 |
R.Anwar,
and
S.Langlois
(2009).
The Arg703Trp missense mutation in F13A1 is a de novo event.
|
| |
Br J Haematol, 146,
118-120.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
A.B.Hervás,
I.Canosa,
and
E.Santero
(2008).
Transcriptome analysis of Pseudomonas putida in response to nitrogen availability.
|
| |
J Bacteriol, 190,
416-420.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
S.Datta,
M.A.Antonyak,
and
R.A.Cerione
(2006).
Importance of Ca(2+)-dependent transamidation activity in the protection afforded by tissue transglutaminase against doxorubicin-induced apoptosis.
|
| |
Biochemistry, 45,
13163-13174.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
C.Esposito,
and
I.Caputo
(2005).
Mammalian transglutaminases. Identification of substrates as a key to physiological function and physiopathological relevance.
|
| |
FEBS J, 272,
615-631.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
E.J.Woo,
Y.G.Kim,
M.S.Kim,
W.D.Han,
S.Shin,
H.Robinson,
S.Y.Park,
and
B.H.Oh
(2004).
Structural mechanism for inactivation and activation of CAD/DFF40 in the apoptotic pathway.
|
| |
Mol Cell, 14,
531-539.
|
 |
|
PDB code:
|
 |
|
|
|
|
|
 |
K.Ginalski,
L.Kinch,
L.Rychlewski,
and
N.V.Grishin
(2004).
BTLCP proteins: a novel family of bacterial transglutaminase-like cysteine proteinases.
|
| |
Trends Biochem Sci, 29,
392-395.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
L.Lorand,
and
R.M.Graham
(2003).
Transglutaminases: crosslinking enzymes with pleiotropic functions.
|
| |
Nat Rev Mol Cell Biol, 4,
140-156.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
H.Okudo,
M.Kito,
T.Moriyama,
T.Ogawa,
and
R.Urade
(2002).
Transglutaminase activity of human ER-60.
|
| |
Biosci Biotechnol Biochem, 66,
1423-1426.
|
 |
|
|
|
|
 |
L.Fesus,
and
M.Piacentini
(2002).
Transglutaminase 2: an enigmatic enzyme with diverse functions.
|
| |
Trends Biochem Sci, 27,
534-539.
|
 |
|
|
|
|
 |
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:
|
 |
|
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
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.
|
 |
|
|
|
|
 |
D.Aeschlimann,
and
V.Thomazy
(2000).
Protein crosslinking in assembly and remodelling of extracellular matrices: the role of transglutaminases.
|
| |
Connect Tissue Res, 41,
1.
|
 |
|
|
|
|
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PDB code:
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PDB code:
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PDB codes:
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PDB code:
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The most recent references are shown first.
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only a partial list as not all journals are covered by
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
code is
shown on the right.
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