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PDBsum entry 1fie

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protein Protein-protein interface(s) links
Transferase PDB id
1fie
Jmol
Contents
Protein chain
705 a.a. *
Waters ×557
* Residue conservation analysis
PDB id:
1fie
Name: Transferase
Title: Recombinant human coagulation factor xiii
Structure: Coagulation factor xiii. Chain: a, b. Fragment: a-subunit (thrombin-cleaved). 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:
2.50Å     R-factor:   0.182    
Authors: V.C.Yee,D.C.Teller
Key ref: V.C.Yee et al. (1995). Structural evidence that the activation peptide is not released upon thrombin cleavage of factor XIII. Thromb Res, 78, 389-397. PubMed id: 7660355
Date:
24-Aug-96     Release date:   12-Feb-97    
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.
705 a.a.*
Key:    PfamA domain  PfamB 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: Ca(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   4 terms 
  Biological process     hemostasis   5 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
Thromb Res 78:389-397 (1995)
PubMed id: 7660355  
 
 
Structural evidence that the activation peptide is not released upon thrombin cleavage of factor XIII.
V.C.Yee, L.C.Pedersen, P.D.Bishop, R.E.Stenkamp, D.C.Teller.
 
  ABSTRACT  
 
The three-dimensional structure of the recombinant human factor XIII a2 dimer after cleavage by thrombin has been determined by X-ray crystallography. Factor XIII zymogen was treated with bovine alpha-thrombin in the presence of 3 mM CaCl2, and the cleaved protein was crystallized from Tris buffered at pH 6.5 using ethanol as the precipitating agent. Refinement of the molecular model of thrombin-cleaved factor XIII against diffraction data from 10.0 to 2.5 A resolution has been carried out to give a crystallographic R factor of 18.2%. The structure of thrombin-cleaved factor XIII is remarkably similar to that of the zymogen: there are no large conformational changes in the protein and the 37 residue amino terminus activation peptide remains associated with the rest of the molecule. This work shows that the activation peptide, upon thrombin cleavage, has the same conformation and occupies the same position with respect to the rest of the molecule as it does in the zymogen structure.
 

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.  
20722598 B.A.Wilson, and M.Ho (2010).
Recent insights into Pasteurella multocida toxin and other G-protein-modulating bacterial toxins.
  Future Microbiol, 5, 1185-1201.  
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.  
20218626 M.A.Jadhav, G.Isetti, T.A.Trumbo, and M.C.Maurer (2010).
Effects of introducing fibrinogen Aalpha character into the factor XIII activation peptide segment.
  Biochemistry, 49, 2918-2924.  
19937244 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.  
  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.  
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.  
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.  
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.  
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
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.  
10455172 T.S.Lai, T.F.Slaughter, K.A.Peoples, and C.S.Greenberg (1999).
Site-directed mutagenesis of the calcium-binding site of blood coagulation factor XIIIa.
  J Biol Chem, 274, 24953-24958.  
9593710 E.Candi, G.Melino, A.Lahm, R.Ceci, A.Rossi, I.G.Kim, B.Ciani, and P.M.Steinert (1998).
Transglutaminase 1 mutations in lamellar ichthyosis. Loss of activity due to failure of activation by proteolytic processing.
  J Biol Chem, 273, 13693-13702.  
9603949 O.V.Mitkevich, J.R.Shainoff, P.M.DiBello, V.C.Yee, D.C.Teller, G.B.Smejkal, P.D.Bishop, I.S.Kolotushkina, K.Fickenscher, and G.P.Samokhin (1998).
Coagulation factor XIIIa undergoes a conformational change evoked by glutamine substrate. Studies on kinetics of inhibition and binding of XIIIA by a cross-reacting antifibrinogen antibody.
  J Biol Chem, 273, 14387-14391.  
9016719 V.C.Yee, K.P.Pratt, H.C.Côté, I.L.Trong, D.W.Chung, E.W.Davie, R.E.Stenkamp, and D.C.Teller (1997).
Crystal structure of a 30 kDa C-terminal fragment from the gamma chain of human fibrinogen.
  Structure, 5, 125-138.
PDB codes: 1fib 1fic 1fid
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.