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PDBsum entry 1k9x
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protein Protein-protein interface(s) links
Carboxypeptidase PDB id
1k9x

 

 

 

 

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Contents
Protein chains
497 a.a. *
Waters ×609
* Residue conservation analysis
PDB id:
1k9x
Name: Carboxypeptidase
Title: Structure of pyrococcus furiosus carboxypeptidase apo-yb
Structure: M32 carboxypeptidase. Chain: a, b, c, d
Source: Pyrococcus furiosus. Organism_taxid: 2261
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.212     R-free:   0.267
Authors: J.W.Arndt,B.Hao,V.Ramakrishnan,T.Cheng,S.I.Chan,M.K.Chan
Key ref:
J.W.Arndt et al. (2002). Crystal structure of a novel carboxypeptidase from the hyperthermophilic archaeon Pyrococcus furiosus. Structure, 10, 215-224. PubMed id: 11839307 DOI: 10.1016/S0969-2126(02)00698-6
Date:
31-Oct-01     Release date:   06-Nov-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8U3L0  (CBP1_PYRFU) -  Thermostable carboxypeptidase 1 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)
Seq:
Struc: 		499 a.a.
497 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.17.19  - carboxypeptidase Taq.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Release of a C-terminal amino acid with broad specificity, except for -Pro.
      Cofactor: Zn(2+)

 

 
DOI no: 10.1016/S0969-2126(02)00698-6 Structure 10:215-224 (2002)
PubMed id: 11839307  
 
 
Crystal structure of a novel carboxypeptidase from the hyperthermophilic archaeon Pyrococcus furiosus.
J.W.Arndt, B.Hao, V.Ramakrishnan, T.Cheng, S.I.Chan, M.K.Chan.
 
  ABSTRACT  
 
The structure of Pyrococcus furiosus carboxypeptidase (PfuCP) has been determined to 2.2 A resolution using multiwavelength anomalous diffraction (MAD) methods. PfuCP represents the first structure of the new M32 family of carboxypeptidases. The overall structure is comprised of a homodimer. Each subunit is mostly helical with its most pronounced feature being a deep substrate binding groove. The active site lies at the bottom of this groove and contains an HEXXH motif that coordinates the metal ion required for catalysis. Surprisingly, the structure is similar to the recently reported rat neurolysin. Comparison of these structures as well as sequence analyses with other homologous proteins reveal several conserved residues. The roles for these conserved residues in the catalytic mechanism are inferred based on modeling and their location.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. PfuCP Subunit Structure(A) Ribbons diagram of a single PfuCP subunit as viewed along the substrate groove. Drawn in stereo (active site metal, pink).(B) Surface diagram of PfuCP subunit in stereo (negatively charged residues, red; positively charged residues, blue) modeled with 10-mer polyalanine substrate.(C) Rainbow stereo plot of the C[a] trace of PfuCP subunit (N terminus, blue; C terminus, red; active site metal, pink). Every twentieth residue is labeled. Figures were prepared using the programs MOLSCRIPT, Raster-3D, and GRASP [11, 29 and 35].
 
  The above figure is reprinted by permission from Cell Press: Structure (2002, 10, 215-224) copyright 2002.  
  Figure was selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18539138 C.E.Isaza, X.Zhong, L.E.Rosas, J.D.White, R.P.Chen, G.F.Liang, S.I.Chan, A.R.Satoskar, and M.K.Chan (2008).
A proposed role for Leishmania major carboxypeptidase in peptide catabolism.
  Biochem Biophys Res Commun, 373, 25-29.  
16717414 H.S.Lee, Y.J.Kim, S.S.Bae, J.H.Jeon, J.K.Lim, S.G.Kang, and J.H.Lee (2006).
Overexpression and characterization of a carboxypeptidase from the hyperthermophilic archaeon Thermococcus sp. NA1.
  Biosci Biotechnol Biochem, 70, 1140-1147.  
16438678 R.E.De Castro, J.A.Maupin-Furlow, M.I.Giménez, M.K.Herrera Seitz, and J.J.Sánchez (2006).
Haloarchaeal proteases and proteolytic systems.
  FEMS Microbiol Rev, 30, 17-35.  
15811801 H.Atomi (2005).
Recent progress towards the application of hyperthermophiles and their enzymes.
  Curr Opin Chem Biol, 9, 166-173.  
14998993 K.Ray, C.S.Hines, J.Coll-Rodriguez, and D.W.Rodgers (2004).
Crystal structure of human thimet oligopeptidase provides insight into substrate recognition, regulation, and localization.
  J Biol Chem, 279, 20480-20489.
PDB code: 1s4b
14754895 P.Towler, B.Staker, S.G.Prasad, S.Menon, J.Tang, T.Parsons, D.Ryan, M.Fisher, D.Williams, N.A.Dales, M.A.Patane, and M.W.Pantoliano (2004).
ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis.
  J Biol Chem, 279, 17996-18007.
PDB codes: 1r42 1r4l
12915047 K.Brew (2003).
Structure of human ACE gives new insights into inhibitor binding and design.
  Trends Pharmacol Sci, 24, 391-394.  
14668810 K.R.Acharya, E.D.Sturrock, J.F.Riordan, and M.R.Ehlers (2003).
Ace revisited: a new target for structure-based drug design.
  Nat Rev Drug Discov, 2, 891-902.  
12605218 N.M.Hooper, and A.J.Turner (2003).
An ACE structure.
  Nat Struct Biol, 10, 155-157.  
12540854 R.Natesh, S.L.Schwager, E.D.Sturrock, and K.R.Acharya (2003).
Crystal structure of the human angiotensin-converting enzyme-lisinopril complex.
  Nature, 421, 551-554.
PDB codes: 1o86 1o8a
12685804 D.W.Moskowitz (2002).
Is "somatic" angiotensin I-converting enzyme a mechanosensor?
  Diabetes Technol Ther, 4, 841-858.  
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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