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Coagulation factor PDB id
1f13
Jmol
Contents
Protein chains
722 a.a. *
Waters ×487
* Residue conservation analysis
PDB id:
1f13
Name: Coagulation factor
Title: Recombinant human cellular coagulation factor xiii
Structure: Cellular coagulation factor xiii zymogen. Chain: a, b. Fragment: a2-homodimer. Synonym: cfxiii. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Organ: placenta. Expressed in: saccharomyces cerevisiae. Expression_system_taxid: 4932
Biol. unit: Dimer (from PQS)
Resolution:
2.10Å     R-factor:   0.183     R-free:   0.236
Authors: M.S.Weiss,R.Hilgenfeld
Key ref:
M.S.Weiss et al. (1998). Two non-proline cis peptide bonds may be important for factor XIII function. FEBS Lett, 423, 291-296. PubMed id: 9515726 DOI: 10.1016/S0014-5793(98)00098-2
Date:
16-Jan-98     Release date:   12-Aug-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00488  (F13A_HUMAN) -  Coagulation factor XIII A chain
Seq:
Struc: 		 
Seq:
Struc: 		732 a.a.
722 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.3.2.13  - Protein-glutamine gamma-glutamyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein glutamine + alkylamine = protein N5-alkylglutamine + NH3
Protein glutamine
 + alkylamine
 = protein N(5)-alkylglutamine
 + NH(3)
      Cofactor: Calcium
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   3 terms 
  Biological process     wound healing   5 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0014-5793(98)00098-2 FEBS Lett 423:291-296 (1998)
PubMed id: 9515726  
 
 
Two non-proline cis peptide bonds may be important for factor XIII function.
M.S.Weiss, H.J.Metzner, R.Hilgenfeld.
 
  ABSTRACT  
 
The structure of recombinant human cellular factor XIII zymogen was solved in its monoclinic crystal form and refined to an R-factor of 18.3% (Rfree = 23.6%) for all data between 40.0 and 2.1 A resolution. Two non-proline cis peptide bonds were detected. One is between Arg310 and Tyr311 close to the active site cysteine residue (Cys314) and the other is between Gln425 and Phe426 at the dimerization interface. The structure and the role of these cis peptides are discussed in the light of their possible importance for factor XIII function.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Overall structure of the factor XIII dimer. The position of the local twofold axis is indicated by (). Within one subunit, the four domains are coloured in yellow, red, green and blue, respectively. The sites of the cis peptide bonds are emphasized by *. The figure was produced using the program MOLSCRIPT [28]. 		Figure 4.
Fig. 4. Sequence alignment of human factor XIII with representative transglutaminases in the regions of the cis peptide bonds. The code given is the SWISSPROT database code, and the identity is with respect to the alignment against factor XIII. The number of amino acids denotes the total length of the aligned region. The residues directly flanking the cis peptide bonds are inside the boxes.
 
  The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (1998, 423, 291-296) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20880254 I.Komáromi, Z.Bagoly, and L.Muszbek (2011).
Factor XIII: novel structural and functional aspects.
  J Thromb Haemost, 9, 9.  
20375315 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.  
  20944217 G.W.Han, M.A.Elsliger, T.O.Yeates, Q.Xu, A.G.Murzin, S.S.Krishna, L.Jaroszewski, P.Abdubek, T.Astakhova, H.L.Axelrod, D.Carlton, C.Chen, H.J.Chiu, T.Clayton, D.Das, M.C.Deller, L.Duan, D.Ernst, J.Feuerhelm, J.C.Grant, A.Grzechnik, K.K.Jin, H.A.Johnson, H.E.Klock, M.W.Knuth, P.Kozbial, A.Kumar, W.W.Lam, D.Marciano, D.McMullan, M.D.Miller, A.T.Morse, E.Nigoghossian, L.Okach, R.Reyes, C.L.Rife, N.Sefcovic, H.J.Tien, C.B.Trame, H.van den Bedem, D.Weekes, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2010).
Structure of a putative NTP pyrophosphohydrolase: YP_001813558.1 from Exiguobacterium sibiricum 255-15.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 1237-1244.
PDB code: 3nl9
20812289 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.  
  20179087 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.  
18982407 R.J.Collighan, and M.Griffin (2009).
Transglutaminase 2 cross-linking of matrix proteins: biological significance and medical applications.
  Amino Acids, 36, 659-670.  
  20160946 S.P.Mielke, and V.V.Krishnan (2009).
Characterization of protein secondary structure from NMR chemical shifts.
  Prog Nucl Magn Reson Spectrosc, 54, 141-165.  
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.  
18544639 K.A.Johnson, D.M.Rose, and R.A.Terkeltaub (2008).
Factor XIIIA mobilizes transglutaminase 2 to induce chondrocyte hypertrophic differentiation.
  J Cell Sci, 121, 2256-2264.  
  18391421 R.Assenberg, O.Delmas, S.C.Graham, A.Verma, N.Berrow, D.I.Stuart, R.J.Owens, H.Bourhy, and J.M.Grimes (2008).
Expression, purification and crystallization of a lyssavirus matrix (M) protein.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 258-262.  
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.  
17057349 A.Wagner, M.Pieren, C.Schulze-Briese, K.Ballmer-Hofer, and A.E.Prota (2006).
Structure determination of VEGF-E by sulfur SAD.
  Acta Crystallogr D Biol Crystallogr, 62, 1430-1434.  
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.  
14648616 H.J.Lee, J.H.Kim, H.J.Jung, K.Y.Kim, E.J.Kim, Y.S.Choi, and C.J.Yoon (2004).
Computational study of conformational preferences of thioamide-containing azaglycine peptides.
  J Comput Chem, 25, 169-178.  
14997549 I.Hudáky, Z.Gáspári, O.Carugo, M.Cemazar, S.Pongor, and A.Perczel (2004).
Vicinal disulfide bridge conformers by experimental methods and by ab initio and DFT molecular computations.
  Proteins, 55, 152-168.  
14993675 Z.Q.Fu, J.P.Rose, and B.C.Wang (2004).
Monitoring the anomalous scattering signal and noise levels in X-ray diffraction of crystals.
  Acta Crystallogr D Biol Crystallogr, 60, 499-506.  
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.  
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
12368090 L.Fesus, and M.Piacentini (2002).
Transglutaminase 2: an enigmatic enzyme with diverse functions.
  Trends Biochem Sci, 27, 534-539.  
12221081 T.Kashiwagi, K.Yokoyama, K.Ishikawa, K.Ono, D.Ejima, H.Matsui, and E.Suzuki (2002).
Crystal structure of microbial transglutaminase from Streptoverticillium mobaraense.
  J Biol Chem, 277, 44252-44260.
PDB code: 1iu4
11867617 Z.Balklava, E.Verderio, R.Collighan, S.Gross, J.Adams, and M.Griffin (2002).
Analysis of tissue transglutaminase function in the migration of Swiss 3T3 fibroblasts: the active-state conformation of the enzyme does not affect cell motility but is important for its secretion.
  J Biol Chem, 277, 16567-16575.  
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.  
11320309 M.S.Weiss, T.Sicker, K.Djinovic-Carugo, and R.Hilgenfeld (2001).
On the routine use of soft X-rays in macromolecular crystallography.
  Acta Crystallogr D Biol Crystallogr, 57, 689-695.  
9988734 B.A.Fox, V.C.Yee, L.C.Pedersen, I.Le Trong, P.D.Bishop, R.E.Stenkamp, and D.C.Teller (1999).
Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor XIII by x-ray crystallography.
  J Biol Chem, 274, 4917-4923.
PDB codes: 1bl2 1ggu 1ggy 1qrk
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
9628859 M.A.Schumacher, D.Carter, D.M.Scott, D.S.Roos, B.Ullman, and R.G.Brennan (1998).
Crystal structures of Toxoplasma gondii uracil phosphoribosyltransferase reveal the atomic basis of pyrimidine discrimination and prodrug binding.
  EMBO J, 17, 3219-3232.
PDB codes: 1bd3 1bd4 1upf 1upu
9699627 M.S.Weiss, A.Jabs, and R.Hilgenfeld (1998).
Peptide bonds revisited.
  Nat Struct Biol, 5, 676.  
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 code is shown on the right.