spacer
spacer

PDBsum entry 1kli
Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
1kli

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
61 a.a. *
254 a.a. *
Ligands
SO4 ×4
BEN
GOL
Metals
_CA
Waters ×299
* Residue conservation analysis
PDB id:
1kli
Name: Hydrolase
Title: Cofactor-and substrate-assisted activation of factor viia
Structure: Factor viia. Chain: l. Fragment: light chain. Engineered: yes. Other_details: n-terminal truncation. Factor viia. Chain: h. Fragment: heavy chain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PQS)
Resolution:
1.69Å     R-factor:   0.209     R-free:   0.225
Authors: K.Sichler,D.W.Banner,A.D'Arcy,K.P.Hopfner,R.Huber,W.Bode,G.B.Kresse, E.Kopetzki,H.Brandstetter
Key ref:
K.Sichler et al. (2002). Crystal structures of uninhibited factor VIIa link its cofactor and substrate-assisted activation to specific interactions. J Mol Biol, 322, 591-603. PubMed id: 12225752 DOI: 10.1016/S0022-2836(02)00747-7
Date:
12-Dec-01     Release date:   18-Sep-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P08709  (FA7_HUMAN) -  Coagulation factor VII from Homo sapiens
Seq:
Struc: 		466 a.a.
61 a.a.
Protein chain
Pfam   ArchSchema ?
P08709  (FA7_HUMAN) -  Coagulation factor VII from Homo sapiens
Seq:
Struc: 		466 a.a.
254 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains L, H: E.C.3.4.21.21  - coagulation factor VIIa.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolyzes one Arg-|-Ile bond in factor X to form factor Xa.

 

 
DOI no: 10.1016/S0022-2836(02)00747-7 J Mol Biol 322:591-603 (2002)
PubMed id: 12225752  
 
 
Crystal structures of uninhibited factor VIIa link its cofactor and substrate-assisted activation to specific interactions.
K.Sichler, D.W.Banner, A.D'Arcy, K.P.Hopfner, R.Huber, W.Bode, G.B.Kresse, E.Kopetzki, H.Brandstetter.
 
  ABSTRACT  
 
Factor VIIa initiates the extrinsic coagulation cascade; this event requires a delicately balanced regulation that is implemented on different levels, including a sophisticated multi-step activation mechanism of factor VII. Its central role in hemostasis and thrombosis makes factor VIIa a key target of pharmaceutical research. We succeeded, for the first time, in recombinantly producing N-terminally truncated factor VII (rf7) in an Escherichia coli expression system by employing an oxidative, in vitro, folding protocol, which depends critically on the presence of ethylene glycol. Activated recombinant factor VIIa (rf7a) was crystallised in the presence of the reversible S1-site inhibitor benzamidine. Comparison of this 1.69A crystal structure with that of an inhibitor-free and sulphate-free, but isomorphous crystal form identified structural details of factor VIIa stimulation. The stabilisation of Asp189-Ser190 by benzamidine and the capping of the intermediate helix by a sulphate ion appear to be sufficient to mimic the disorder-order transition conferred by the cofactor tissue factor (TF) and the substrate factor X. Factor VIIa shares with the homologous factor IXa, but not factor Xa, a bell-shaped activity modulation dependent on ethylene glycol. The ethylene glycol-binding site of rf7a was identified in the vicinity of the 60 loop. Ethylene glycol binding induces a significant conformational rearrangement of the 60 loop. This region serves as a recognition site of the physiologic substrate, factor X, which is common to both factor VIIa and factor IXa. These results provide a mechanistic framework of substrate-assisted catalysis of both factor VIIa and factor IXa.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Overview of rf7a^BA. The protein is shown in ribbon representation (blue, catalytic domain, grey, EGF2-domain), the residues of the catalytic triad, the inhibitor benzamidine, the four sulphate groups and the glycerol moiety are shown in stick representation, and the calcium ion is shown as a green ball. 		Figure 7.
Figure 7. A stereo view of the 170 loop and the intermediate helix. Orange, arrow pointing to the intermediate helix (Met164-Ser170B) and Ser170H-Cys182; pink, insertion loop (Arg170C-Asp170G); green, Trp215-Arg230; purple, sulphate; light blue, disulfide bond Cys168-Cys182; white ball, water. Residues Met164, Cys168, Gln170A-Asn175, Cys182, Trp215 and Arg230 are shown including their side-chains, for the other residues, only the backbone atoms are shown. The factor VIIa specific insertion loop Arg170C-Asp170G and the sulphate groups are shown with their 2F[o] -F[c] electron density maps. The hydrogen bonds stabilising the sulphate groups are indicated by white dotted lines.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 322, 591-603) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21406063 C.S.Craik, M.J.Page, and E.L.Madison (2011).
Proteases as therapeutics.
  Biochem J, 435, 1.  
20615447 P.Goettig, V.Magdolen, and H.Brandstetter (2010).
Natural and synthetic inhibitors of kallikrein-related peptidases (KLKs).
  Biochimie, 92, 1546-1567.  
19490111 E.Persson, and O.H.Olsen (2009).
Activation loop 3 and the 170 loop interact in the active conformation of coagulation factor VIIa.
  FEBS J, 276, 3099-3109.  
19361276 T.Zögg, and H.Brandstetter (2009).
Activation mechanisms of coagulation factor IX.
  Biol Chem, 390, 391-400.  
20004170 T.Zögg, and H.Brandstetter (2009).
Structural basis of the cofactor- and substrate-assisted activation of human coagulation factor IXa.
  Structure, 17, 1669-1678.
PDB codes: 2wph 2wpi 2wpj 2wpk 2wpl 2wpm
17384232 O.H.Olsen, K.D.Rand, H.Østergaard, and E.Persson (2007).
A combined structural dynamics approach identifies a putative switch in factor VIIa employed by tissue factor to initiate blood coagulation.
  Protein Sci, 16, 671-682.  
17002651 C.M.Colina, D.Venkateswarlu, R.Duke, L.Perera, and L.G.Pedersen (2006).
What causes the enhancement of activity of factor VIIa by tissue factor?
  J Thromb Haemost, 4, 2726-2729.  
16687401 K.D.Rand, T.J.Jørgensen, O.H.Olsen, E.Persson, O.N.Jensen, H.R.Stennicke, and M.D.Andersen (2006).
Allosteric activation of coagulation factor VIIa visualized by hydrogen exchange.
  J Biol Chem, 281, 23018-23024.  
16757484 S.P.Bajaj, A.E.Schmidt, S.Agah, M.S.Bajaj, and K.Padmanabhan (2006).
High resolution structures of p-aminobenzamidine- and benzamidine-VIIa/soluble tissue factor: unpredicted conformation of the 192-193 peptide bond and mapping of Ca2+, Mg2+, Na+, and Zn2+ sites in factor VIIa.
  J Biol Chem, 281, 24873-24888.
PDB codes: 2a2q 2aer 2fir
15632123 A.G.Olivero, C.Eigenbrot, R.Goldsmith, K.Robarge, D.R.Artis, J.Flygare, T.Rawson, D.P.Sutherlin, S.Kadkhodayan, M.Beresini, L.O.Elliott, G.G.DeGuzman, D.W.Banner, M.Ultsch, U.Marzec, S.R.Hanson, C.Refino, S.Bunting, and D.Kirchhofer (2005).
A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo.
  J Biol Chem, 280, 9160-9169.
PDB code: 1ygc
15840825 H.R.Maun, C.Eigenbrot, H.Raab, D.Arnott, L.Phu, S.Bullens, and R.A.Lazarus (2005).
Disulfide locked variants of factor VIIa with a restricted beta-strand conformation have enhanced enzymatic activity.
  Protein Sci, 14, 1171-1180.  
15667541 J.Hewitt, J.N.Ballard, T.N.Nelson, V.C.Smith, T.A.Griffiths, S.Pritchard, J.K.Wu, L.D.Wadsworth, B.Casey, and R.T.MacGillivray (2005).
Severe FVII deficiency caused by a new point mutation combined with a previously undetected gene deletion.
  Br J Haematol, 128, 380-385.  
16241939 M.J.Page, R.T.Macgillivray, and E.Di Cera (2005).
Determinants of specificity in coagulation proteases.
  J Thromb Haemost, 3, 2401-2408.  
15892855 W.Bode (2005).
The structure of thrombin, a chameleon-like proteinase.
  J Thromb Haemost, 3, 2379-2388.  
15152000 A.O.Pineda, C.J.Carrell, L.A.Bush, S.Prasad, S.Caccia, Z.W.Chen, F.S.Mathews, and E.Di Cera (2004).
Molecular dissection of Na+ binding to thrombin.
  J Biol Chem, 279, 31842-31853.
PDB codes: 1sfq 1sg8 1sgi 1shh
15566361 F.Peyvandi, R.De Cristofaro, I.Garagiola, R.Palla, S.Akhavan, R.Landolfi, and P.M.Mannucci (2004).
The P303T mutation in the human factor VII (FVII) gene alters the conformational state of the enzyme and causes a severe functional deficiency.
  Br J Haematol, 127, 576-584.  
14750250 M.V.Midathada, P.Mehta, M.Waner, and L.M.Fink (2004).
Recombinant factor VIIa in the treatment of bleeding.
  Am J Clin Pathol, 121, 124-137.  
12444082 K.Sichler, E.Kopetzki, R.Huber, W.Bode, K.P.Hopfner, and H.Brandstetter (2003).
Physiological fIXa activation involves a cooperative conformational rearrangement of the 99-loop.
  J Biol Chem, 278, 4121-4126.  
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.

 

spacer
spacer