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PDBsum entry 3d68
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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
3d68

 

 

 

 

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Contents
Protein chain
401 a.a. *
Ligands
NAG ×11
ARG ×3
Metals
_ZN ×3
* Residue conservation analysis
PDB id:
3d68
Name: Hydrolase
Title: Crystal structure of a t325i/t329i/h333y/h335q mutant of thrombin- activatable fibrinolysis inhibitor (tafi-iiyq)
Structure: Carboxypeptidase b2. Chain: a, b, c. Fragment: tafi-iiyq, unp residues 24-423. Synonym: carboxypeptidase u, cpu, thrombin-activable fibrinolysis inhibitor, tafi, plasma carboxypeptidase b, pcpb. Engineered: yes. Mutation: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: cpb2. Expressed in: homo sapiens. Expression_system_taxid: 9606. Expression_system_cell_line: hek293es. Expression_system_cell: embryonic kidney cell.
Resolution:
2.80Å     R-factor:   0.190     R-free:   0.232
Authors: T.H.C.Brondijk,E.G.Huizinga
Key ref: P.F.Marx et al. (2008). Crystal structures of TAFI elucidate the inactivation mechanism of activated TAFI: a novel mechanism for enzyme autoregulation. Blood, 112, 2803-2809. PubMed id: 18559974
Date:
19-May-08     Release date:   01-Jul-08    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q96IY4  (CBPB2_HUMAN) -  Carboxypeptidase B2 from Homo sapiens
Seq:
Struc: 		423 a.a.
401 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.17.20  - carboxypeptidase U.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Release of C-terminal Arg and Lys from a polypeptide.
      Cofactor: Zn(2+)

 

 
Blood 112:2803-2809 (2008)
PubMed id: 18559974  
 
 
Crystal structures of TAFI elucidate the inactivation mechanism of activated TAFI: a novel mechanism for enzyme autoregulation.
P.F.Marx, T.H.Brondijk, T.Plug, R.A.Romijn, W.Hemrika, J.C.Meijers, E.G.Huizinga.
 
  ABSTRACT  
 
Thrombin-activatable fibrinolysis inhibitor (TAFI) is a pro-metallocarboxypeptidase that can be proteolytically activated (TAFIa). TAFIa is unique among carboxypeptidases in that it spontaneously inactivates with a short half-life, a property that is crucial for its role in controlling blood clot lysis. We studied the intrinsic instability of TAFIa by solving crystal structures of TAFI, a TAFI inhibitor (GEMSA) complex and a quadruple TAFI mutant (70-fold more stable active enzyme). The crystal structures show that TAFIa stability is directly related to the dynamics of a 55-residue segment (residues 296-350) that includes residues of the active site wall. Dynamics of this flap are markedly reduced by the inhibitor GEMSA, a known stabilizer of TAFIa, and stabilizing mutations. Our data provide the structural basis for a model of TAFI auto-regulation: in zymogen TAFI the dynamic flap is stabilized by interactions with the activation peptide. Release of the activation peptide increases dynamic flap mobility and in time this leads to conformational changes that disrupt the catalytic site and expose a cryptic thrombin-cleavage site present at Arg302. This represents a novel mechanism of enzyme control that enables TAFI to regulate its activity in plasma in the absence of specific inhibitors.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19802820 D.Fernández, E.Boix, I.Pallarès, F.X.Avilés, and J.Vendrell (2010).
Analysis of a new crystal form of procarboxypeptidase B: Further insights into the catalytic mechanism.
  Biopolymers, 93, 178-185.
PDB code: 3glj
20704647 M.Valls Serón, J.Haiko, P.G.DE Groot, T.K.Korhonen, and J.C.Meijers (2010).
Thrombin-activatable fibrinolysis inhibitor is degraded by Salmonella enterica and Yersinia pestis.
  J Thromb Haemost, 8, 2232-2240.  
19874466 R.Brouns, E.Heylen, J.L.Willemse, R.Sheorajpanday, D.De Surgeloose, R.Verkerk, P.P.De Deyn, and D.F.Hendriks (2010).
The decrease in procarboxypeptidase U (TAFI) concentration in acute ischemic stroke correlates with stroke severity, evolution and outcome.
  J Thromb Haemost, 8, 75-80.  
20237223 R.Cagliani, M.Fumagalli, S.Riva, U.Pozzoli, M.Fracassetti, N.Bresolin, G.P.Comi, and M.Sironi (2010).
Polymorphisms in the CPB2 gene are maintained by balancing selection and result in haplotype-preferential splicing of exon 7.
  Mol Biol Evol, 27, 1945-1954.  
19074424 C.Wu, P.Y.Kim, R.Manuel, M.Seto, M.Whitlow, M.Nagashima, J.Morser, A.Gils, P.Declerck, and M.E.Nesheim (2009).
The roles of selected arginine and lysine residues of TAFI (Pro-CPU) in its activation to TAFIa by the thrombin-thrombomodulin complex.
  J Biol Chem, 284, 7059-7067.  
19017261 D.C.Rijken, and H.R.Lijnen (2009).
New insights into the molecular mechanisms of the fibrinolytic system.
  J Thromb Haemost, 7, 4.  
19214510 D.Caramazza, C.Caracciolo, R.Barone, A.Malato, G.Saccullo, V.Cigna, S.Berretta, L.Schinocca, G.Quintini, V.Abbadessa, F.Di Raimondo, and S.Siragusa (2009).
Correlation between leukocytosis and thrombosis in Philadelphia-negative chronic myeloproliferative neoplasms.
  Ann Hematol, 88, 967-971.  
18941109 J.Bestebroer, K.P.van Kessel, H.Azouagh, A.M.Walenkamp, I.G.Boer, R.A.Romijn, J.A.van Strijp, and C.J.de Haas (2009).
Staphylococcal SSL5 inhibits leukocyte activation by chemokines and anaphylatoxins.
  Blood, 113, 328-337.  
  19377074 M.E.Meltzer, C.J.Doggen, P.G.de Groot, J.C.Meijers, F.R.Rosendaal, and T.Lisman (2009).
Low thrombin activatable fibrinolysis inhibitor activity levels are associated with an increased risk of a first myocardial infarction in men.
  Haematologica, 94, 811-818.  
19335449 M.F.Miah, and M.B.Boffa (2009).
Functional analysis of mutant variants of thrombin-activatable fibrinolysis inhibitor resistant to activation by thrombin or plasmin.
  J Thromb Haemost, 7, 665-672.  
19054324 P.F.Marx, T.Plug, S.R.Havik, M.Mörgelin, and J.C.Meijers (2009).
The activation peptide of thrombin-activatable fibrinolysis inhibitor: a role in activity and stability of the enzyme?
  J Thromb Haemost, 7, 445-452.  
19416536 Z.Valnickova, M.Thaysen-Andersen, P.Højrup, T.Christensen, K.W.Sanggaard, T.Kristensen, and J.J.Enghild (2009).
Biochemical characterization of bovine plasma thrombin-activatable fibrinolysis inhibitor (TAFI).
  BMC Biochem, 10, 13.  
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.

 

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