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PDBsum entry 6cpa

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protein ligands metals links
Hydrolase (c-terminal peptidase) PDB id
6cpa
Jmol
Contents
Protein chain
307 a.a. *
Ligands
ZAF
Metals
_ZN
Waters ×148
* Residue conservation analysis
PDB id:
6cpa
Name: Hydrolase (c-terminal peptidase)
Title: Crystal structure of the complex of carboxypeptidase a with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes
Structure: Carboxypeptidase a. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Resolution:
2.00Å     R-factor:   0.193    
Authors: H.Kim,W.N.Lipscomb
Key ref:
H.Kim and W.N.Lipscomb (1990). Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes. Biochemistry, 29, 5546-5555. PubMed id: 2386784 DOI: 10.1021/bi00475a019
Date:
15-Feb-90     Release date:   15-Oct-91    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00730  (CBPA1_BOVIN) -  Carboxypeptidase A1
Seq:
Struc:
419 a.a.
307 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.4.17.1  - Carboxypeptidase A.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Peptidyl-L-amino acid + H2O = peptide + L-amino acid

+
=
+
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     proteolysis   1 term 
  Biochemical function     zinc ion binding     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi00475a019 Biochemistry 29:5546-5555 (1990)
PubMed id: 2386784  
 
 
Crystal structure of the complex of carboxypeptidase A with a strongly bound phosphonate in a new crystalline form: comparison with structures of other complexes.
H.Kim, W.N.Lipscomb.
 
  ABSTRACT  
 
O-[[(1R)-[[N-(Phenylmethoxycarbonyl)-L-alanyl]amino]ethyl] hydroxyphosphinyl]-L-3-phenyllacetate [ZAAP(O)F], an analogue of (benzyloxycarbonyl)-Ala-Ala-Phe or (benzyloxycarbonyl)-Ala-Ala-phenyllactate, binds to carboxypeptidase A with great affinity (Ki = 3 pM). Similar phosphonates have been shown to be transition-state analogues of the CPA-catalyzed hydrolysis [Hanson, J. E., Kaplan, A. P., & Bartlett, P. A. (1989) Biochemistry 28, 6294-6305]. In the present study, the structure of the complex of this phosphonate with carboxypeptidase A has been determined by X-ray crystallography to a resolution of 2.0 A. The complex crystallizes in the space group P2(1)2(1)2(1) with cell dimensions a = 61.9 A, b = 67.2 A, and c = 76.2 A. The structure of the complex was solved by molecular replacement. Refinement of the structure against 20,776 unique reflections between 10.0 and 2.0 A yields a crystallographic residual of 0.193, including 140 water molecules. The two phosphinyl oxygens of the inhibitor bind to the active-site zinc at 2.2 A on the electrophilic (Arg-127) side and 3.1 A on the nucleophilic (Glu-270) side. Various features of the binding mode of this phosphonate inhibitor are consistent with the hypothesis that carboxypeptidase A catalyzed hydrolysis proceeds through a general-base mechanism in which the carbonyl carbon of the substrate is attacked by Zn-hydroxyl (or Zn-water). An unexpected feature of the bound inhibitor, the cis carbamoyl ester bond at the benzyloxycarbonyl linkage to alanine, allows the benzyloxycarbonyl phenyl ring of the inhibitor to interact favorably with Tyr-198. This complex structure is compared with previous structures of carboxypeptidase A, including the complexes with the potato inhibitor, a hydrated keto methylene substrate analogue, and a phosphonamidate inhibitor. Comparisons are also made with the complexes of thermolysin with some phosphonamidate inhibitors.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20229282 D.Haller, P.Ekici, A.Friess, and H.Parlar (2010).
High enrichment of MMP-9 and carboxypeptidase A by tweezing adsorptive bubble separation (TABS).
  Appl Biochem Biotechnol, 162, 1547-1557.  
19552427 D.Xu, and H.Guo (2009).
Quantum mechanical/molecular mechanical and density functional theory studies of a prototypical zinc peptidase (carboxypeptidase A) suggest a general acid-general base mechanism.
  J Am Chem Soc, 131, 9780-9788.  
18566513 I.Pallarès, D.Fernández, M.Comellas-Bigler, J.Fernández-Recio, S.Ventura, F.X.Avilés, W.Bode, and J.Vendrell (2008).
Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid).
  Acta Crystallogr D Biol Crystallogr, 64, 784-791.
PDB code: 2v77
17194761 E.Bitto, C.A.Bingman, G.E.Wesenberg, J.G.McCoy, and G.N.Phillips (2007).
Structure of aspartoacylase, the brain enzyme impaired in Canavan disease.
  Proc Natl Acad Sci U S A, 104, 456-461.
PDB codes: 2gu2 2i3c
17766382 J.Dechancie, F.R.Clemente, A.J.Smith, H.Gunaydin, Y.L.Zhao, X.Zhang, and K.N.Houk (2007).
How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design.
  Protein Sci, 16, 1851-1866.  
17391648 J.R.Hershfield, N.Pattabiraman, C.N.Madhavarao, and M.A.Namboodiri (2007).
Mutational analysis of aspartoacylase: implications for Canavan disease.
  Brain Res, 1148, 1.  
16260742 A.Bayés, M.Comellas-Bigler, M.Rodríguez de la Vega, K.Maskos, W.Bode, F.X.Aviles, M.A.Jongsma, J.Beekwilder, and J.Vendrell (2005).
Structural basis of the resistance of an insect carboxypeptidase to plant protease inhibitors.
  Proc Natl Acad Sci U S A, 102, 16602-16607.
PDB code: 2c1c
15139817 B.Jayaram, and T.Jain (2004).
The role of water in protein-DNA recognition.
  Annu Rev Biophys Biomol Struct, 33, 343-361.  
12586391 N.A.Desai, and V.Shankar (2003).
Single-strand-specific nucleases.
  FEMS Microbiol Rev, 26, 457-491.  
11157230 K.Ishikawa, H.Ishida, I.Matsui, Y.Kawarabayasi, and H.Kikuchi (2001).
Novel bifunctional hyperthermostable carboxypeptidase/aminoacylase from Pyrococcus horikoshii OT3.
  Appl Environ Microbiol, 67, 673-679.  
11223512 T.Hori, T.Kumasaka, M.Yamamoto, N.Nonaka, N.Tanaka, Y.Hashimoto, U.Ueki, and K.Takio (2001).
Structure of a new 'aspzincin' metalloendopeptidase from Grifola frondosa: implications for the catalytic mechanism and substrate specificity based on several different crystal forms.
  Acta Crystallogr D Biol Crystallogr, 57, 361-368.
PDB codes: 1g12 1ge5 1ge6 1ge7
10955996 D.M.van Aalten, C.R.Chong, and L.Joshua-Tor (2000).
Crystal structure of carboxypeptidase A complexed with D-cysteine at 1.75 A - inhibitor-induced conformational changes.
  Biochemistry, 39, 10082-10089.
PDB code: 1f57
  10850800 K.M.Holtz, B.Stec, J.K.Myers, S.M.Antonelli, T.S.Widlanski, and E.R.Kantrowitz (2000).
Alternate modes of binding in two crystal structures of alkaline phosphatase-inhibitor complexes.
  Protein Sci, 9, 907-915.
PDB codes: 1ew8 1ew9
9348662 C.L.Perrin, and J.B.Nielson (1997).
"Strong" hydrogen bonds in chemistry and biology.
  Annu Rev Phys Chem, 48, 511-544.  
9220957 E.Asante-Appiah, J.Seetharaman, F.Sicheri, D.S.Yang, and W.W.Chan (1997).
Gem-dialkyl succinic acids: a novel class of inhibitors for carboxypeptidases.
  Biochemistry, 36, 8710-8715.  
8756323 F.Grams, V.Dive, A.Yiotakis, I.Yiallouros, S.Vassiliou, R.Zwilling, W.Bode, and W.Stöcker (1996).
Structure of astacin with a transition-state analogue inhibitor.
  Nat Struct Biol, 3, 671-675.
PDB codes: 1qji 1qjj
8894106 S.S.Ghosh, S.Dakoji, Y.Tanaka, Y.J.Cho, and S.Mobashery (1996).
Properties of analogues of an intermediate in the process of mechanism-based inactivation of carboxypeptidase A.
  Bioorg Med Chem, 4, 1487-1492.  
7711255 H.Zhang, and R.G.Bryant (1995).
Characterization of enzyme-bound ligand dynamics by solid-state NMR in the presence of ligand exchange: L-phenylalanine on carboxypeptidase A.
  Biophys J, 68, 303-311.  
7964925 H.J.Böhm (1994).
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure.
  J Comput Aided Mol Des, 8, 243-256.  
8436102 F.X.Avilés, J.Vendrell, A.Guasch, M.Coll, and R.Huber (1993).
Advances in metallo-procarboxypeptidases. Emerging details on the inhibition mechanism and on the activation process.
  Eur J Biochem, 211, 381-389.  
1449602 A.L.Osterman, N.V.Grishin, S.V.Smulevitch, M.V.Matz, O.P.Zagnitko, L.P.Revina, and V.M.Stepanov (1992).
Primary structure of carboxypeptidase T: delineation of functionally relevant features in Zn-carboxypeptidase family.
  J Protein Chem, 11, 561-570.  
1521526 A.Teplyakov, K.Polyakov, G.Obmolova, B.Strokopytov, I.Kuranova, A.Osterman, N.Grishin, S.Smulevitch, O.Zagnitko, and O.Galperina (1992).
Crystal structure of carboxypeptidase T from Thermoactinomyces vulgaris.
  Eur J Biochem, 208, 281-288.
PDB code: 1obr
1730223 S.Mangani, P.Carloni, and P.Orioli (1992).
X-ray diffraction study of the interaction between carboxypeptidase A and (S)-(+)-1-amino-2-phenylethyl phosphonic acid.
  Eur J Biochem, 203, 173-177.  
  1710977 A.Volbeda, A.Lahm, F.Sakiyama, and D.Suck (1991).
Crystal structure of Penicillium citrinum P1 nuclease at 2.8 A resolution.
  EMBO J, 10, 1607-1618.  
1367679 J.A.Tainer, V.A.Roberts, and E.D.Getzoff (1991).
Metal-binding sites in proteins.
  Curr Opin Biotechnol, 2, 582-591.  
  1989886 L.S.Beese, and T.A.Steitz (1991).
Structural basis for the 3'-5' exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism.
  EMBO J, 10, 25-33.  
  1989878 M.Coll, A.Guasch, F.X.Avilés, and R.Huber (1991).
Three-dimensional structure of porcine procarboxypeptidase B: a structural basis of its inactivity.
  EMBO J, 10, 1-9.
PDB code: 1nsa
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.