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PDBsum entry 5cpa

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protein metals links
Hydrolase (c-terminal peptidase) PDB id
5cpa
Jmol
Contents
Protein chain
307 a.a. *
Metals
_ZN
Waters ×315
* Residue conservation analysis
PDB id:
5cpa
Name: Hydrolase (c-terminal peptidase)
Title: Refined crystal structure of carboxypeptidase a at 1.54 angstroms resolution.
Structure: Carboxypeptidase a. Chain: a. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913
Resolution:
1.54Å     R-factor:   not given    
Authors: W.N.Lipscomb
Key ref:
D.C.Rees et al. (1983). Refined crystal structure of carboxypeptidase A at 1.54 A resolution. J Mol Biol, 168, 367-387. PubMed id: 6887246 DOI: 10.1016/S0022-2836(83)80024-2
Date:
06-May-82     Release date:   29-Jul-82    
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: Zinc
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: 10.1016/S0022-2836(83)80024-2 J Mol Biol 168:367-387 (1983)
PubMed id: 6887246  
 
 
Refined crystal structure of carboxypeptidase A at 1.54 A resolution.
D.C.Rees, M.Lewis, W.N.Lipscomb.
 
  ABSTRACT  
 
The crystal structure of bovine carboxypeptidase A (Cox) has been refined at 1.54 A resolution using the restrained least-squares algorithm of Hendrickson & Konnert (1981). The crystallographic R factor (formula; see text) for structure factors calculated from the final model is 0.190. Bond lengths and bond angles in the carboxypeptidase A model have root-mean-square deviations from ideal values of 0.025 A and 3.6 degrees, respectively. Four examples of a reverse turn like structure (the "Asx" turn) requiring an aspartic acid or asparagine residue are observed in this structure. The Asx turn has the same number of atoms as a reverse turn, but only one peptide bond, and the hydrogen bond that closes the turn is between the Asx side-chain CO group and a main-chain NH group. The distributions of CO-N and NH-O hydrogen bond angles in the alpha-helices and beta-sheet structures of carboxypeptidase A are centered about 156 degrees. A total of 192 water molecules per molecule of enzyme are included in the final model. Unlike the hydrogen bonding geometry observed in the secondary structure of the enzyme, the CO-O(wat) hydrogen bond angle is distributed about 131 degrees, indicating the role of the lone pair electrons of the carbonyl oxygen in the hydrogen bond interaction. Twenty four solvent molecules are observed buried within the protein. Several of these waters are organized into hydrogen-bonded chains containing up to five waters. The average temperature factor for atoms in carboxypeptidase A is 8 A2, and varies from 5 A2 in the center of the protein, to over 30 A2 at the surface.
 
  Selected figure(s)  
 
Figure 13.
FIG. 13. Stereoview ofthe region surrounding a 5-membered chain ofwater molecules (waters 510, 519, 529, 539 and 548) buried in CPA.
Figure 15.
FIO. 15. Active site region f an (IFo-W:I) difference map illustrating the water structure. All water molecules were omitted from the calculated structure factors.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1983, 168, 367-387) copyright 1983.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20368803 C.M.Stegmann, R.Lührmann, and M.C.Wahl (2010).
The crystal structure of PPIL1 bound to cyclosporine A suggests a binding mode for a linear epitope of the SKIP protein.
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PDB code: 2x7k
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On the origin of the catalytic power of carboxypeptidase A and other metalloenzymes.
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PDB code: 2v77
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A potato carboxypeptidase inhibitor gene provides pathogen resistance in transgenic rice.
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PDB codes: 2g1t 2g2f 2g2h 2g2i
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Crystal structure of prostate-specific membrane antigen, a tumor marker and peptidase.
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PDB code: 1z8l
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PDB code: 1u9r
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Mimicry by asx- and ST-turns of the four main types of beta-turn in proteins.
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Interdomain zinc site on human albumin.
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Refined structure of bovine carboxypeptidase A at 1.25 A resolution.
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PDB code: 1m4l
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PDB code: 1q7l
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Mutations in the substrate binding site of thrombin-activatable fibrinolysis inhibitor (TAFI) alter its substrate specificity.
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Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA.
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PDB codes: 1mbu 1mbv 1mbx
11856302 K.Håkansson, and C.G.Miller (2002).
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PDB code: 1fno
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Site-directed mutagenesis of the bacterial metalloamidase UDP-(3-O-acyl)-N-acetylglucosamine deacetylase (LpxC). Identification of the zinc binding site.
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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.
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PDB code: 1bu3
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Zinc-dependent structural stability of human Sonic hedgehog.
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10545376 U.Ryde (1999).
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PDB codes: 1arl 1arm 1yme
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Zinc enzymes.
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Structural trees for protein superfamilies.
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Gem-dialkyl succinic acids: a novel class of inhibitors for carboxypeptidases.
  Biochemistry, 36, 8710-8715.  
9384570 I.García-Sáez, D.Reverter, J.Vendrell, F.X.Avilés, and M.Coll (1997).
The three-dimensional structure of human procarboxypeptidase A2. Deciphering the basis of the inhibition, activation and intrinsic activity of the zymogen.
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PDB code: 1aye
9245420 S.T.Huang, W.E.Choi, C.Bloom, M.Leuenberger, and M.F.Dunn (1997).
Carboxylate ions are strong allosteric ligands for the HisB10 sites of the R-state insulin hexamer.
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Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
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PDB code: 1boo
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Rationalization of the strength of metal binding to human serum transferrin.
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2D 1H and 3D 1H-15N NMR of zinc-rubredoxins: contributions of the beta-sheet to thermostability.
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Acetylpolyamine amidohydrolase from Mycoplana ramosa: gene cloning and characterization of the metal-substituted enzyme.
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X-ray structures of a designed binding site in trypsin show metal-dependent geometry.
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PDB codes: 1slu 1slv 1slw 1slx
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Induced and spontaneous mutations at Ser202 of carboxypeptidase E. Effect on enzyme expression, activity, and intracellular routing.
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Small structural changes account for the high thermostability of 1[4Fe-4S] ferredoxin from the hyperthermophilic bacterium Thermotoga maritima.
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PDB code: 1vjw
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.  
8534804 J.Antosiewicz (1995).
Computation of the dipole moments of proteins.
  Biophys J, 69, 1344-1354.  
7896805 L.Catasús, J.Vendrell, F.X.Avilés, S.Carreira, A.Puigserver, and M.Billeter (1995).
The sequence and conformation of human pancreatic procarboxypeptidase A2. cDNA cloning, sequence analysis, and three-dimensional model.
  J Biol Chem, 270, 6651-6657.  
8539245 R.H.Stote, and M.Karplus (1995).
Zinc binding in proteins and solution: a simple but accurate nonbonded representation.
  Proteins, 23, 12-31.  
8536678 R.J.Williams (1995).
Energised (entatic) states of groups and of secondary structures in proteins and metalloproteins.
  Eur J Biochem, 234, 363-381.  
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The structure of a Ca(2+)-binding epidermal growth factor-like domain: its role in protein-protein interactions.
  Cell, 82, 131-141.
PDB code: 1edm
7892172 A.M.Mathiowetz, A.Jain, N.Karasawa, and W.A.Goddard (1994).
Protein simulations using techniques suitable for very large systems: the cell multipole method for nonbond interactions and the Newton-Euler inverse mass operator method for internal coordinate dynamics.
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  7756980 E.G.Hutchinson, and J.M.Thornton (1994).
A revised set of potentials for beta-turn formation in proteins.
  Protein Sci, 3, 2207-2216.  
8159667 L.Banci, I.Bertini, and G.La Penna (1994).
The enzymatic mechanism of carboxypeptidase: a molecular dynamics study.
  Proteins, 18, 186-197.  
  7703838 S.A.Moore, and M.N.James (1994).
Common structural features of the luxF protein and the subunits of bacterial luciferase: evidence for a (beta alpha)8 fold in luciferase.
  Protein Sci, 3, 1914-1926.  
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.  
8394001 M.H.Zehfus (1993).
Improved calculations of compactness and a reevaluation of continuous compact units.
  Proteins, 16, 293-300.  
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
1438184 D.Bassolino-Klimas, and R.E.Bruccoleri (1992).
Application of a directed conformational search for generating 3-D coordinates for protein structures from alpha-carbon coordinates.
  Proteins, 14, 465-474.  
  1304880 D.C.Richardson, and J.S.Richardson (1992).
The kinemage: a tool for scientific communication.
  Protein Sci, 1, 3-9.  
1729276 D.S.Reynolds, D.S.Gurley, and K.F.Austen (1992).
Cloning and characterization of the novel gene for mast cell carboxypeptidase A.
  J Clin Invest, 89, 273-282.  
1329276 J.N.Higaki, R.J.Fletterick, and C.S.Craik (1992).
Engineered metalloregulation in enzymes.
  Trends Biochem Sci, 17, 100-104.  
1518800 L.Banci, S.Schröder, and P.A.Kollman (1992).
Molecular dynamics characterization of the active cavity of carboxypeptidase A and some of its inhibitor adducts.
  Proteins, 13, 288-305.  
  1303768 M.W.Day, B.T.Hsu, L.Joshua-Tor, J.B.Park, Z.H.Zhou, M.W.Adams, and D.C.Rees (1992).
X-ray crystal structures of the oxidized and reduced forms of the rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.
  Protein Sci, 1, 1494-1507.
PDB codes: 1caa 1cad
1592116 P.J.Artymiuk, H.M.Grindley, J.E.Park, D.W.Rice, and P.Willett (1992).
Three-dimensional structural resemblance between leucine aminopeptidase and carboxypeptidase A revealed by graph-theoretical techniques.
  FEBS Lett, 303, 48-52.  
1553382 P.J.Baker, K.L.Britton, P.C.Engel, G.W.Farrants, K.S.Lilley, D.W.Rice, and T.J.Stillman (1992).
Subunit assembly and active site location in the structure of glutamate dehydrogenase.
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  1303769 P.R.Blake, J.B.Park, Z.H.Zhou, D.R.Hare, M.W.Adams, and M.F.Summers (1992).
Solution-state structure by NMR of zinc-substituted rubredoxin from the marine hyperthermophilic archaebacterium Pyrococcus furiosus.
  Protein Sci, 1, 1508-1521.
PDB code: 1zrp
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.
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1454840 T.Head-Gordon, F.H.Stillinger, M.H.Wright, and D.M.Gay (1992).
Poly(L-alanine) as a universal reference material for understanding protein energies and structures.
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1633827 W.Stark, R.A.Pauptit, K.S.Wilson, and J.N.Jansonius (1992).
The structure of neutral protease from Bacillus cereus at 0.2-nm resolution.
  Eur J Biochem, 207, 781-791.
PDB code: 1npc
2006137 J.L.Scully, and D.R.Evans (1991).
Comparative modeling of mammalian aspartate transcarbamylase.
  Proteins, 9, 191-206.  
  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
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Side chain-backbone hydrogen bonding contributes to helix stability in peptides derived from an alpha-helical region of carboxypeptidase A.
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1749775 O.Herzberg, and J.Moult (1991).
Analysis of the steric strain in the polypeptide backbone of protein molecules.
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2153297 E.B.Springman, E.L.Angleton, H.Birkedal-Hansen, and H.E.Van Wart (1990).
Multiple modes of activation of latent human fibroblast collagenase: evidence for the role of a Cys73 active-site zinc complex in latency and a "cysteine switch" mechanism for activation.
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2281084 E.G.Hutchinson, and J.M.Thornton (1990).
HERA--a program to draw schematic diagrams of protein secondary structures.
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Where metal ions bind in proteins.
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2166604 M.Nilges, G.M.Clore, and A.M.Gronenborn (1990).
1H-NMR stereospecific assignments by conformational data-base searches.
  Biopolymers, 29, 813-822.  
2160297 T.T.Tibbitts, D.L.Caspar, W.C.Phillips, and D.A.Goodenough (1990).
Diffraction diagnosis of protein folding in gap junction connexons.
  Biophys J, 57, 1025-1036.  
2395868 V.A.Roberts, B.L.Iverson, S.A.Iverson, S.J.Benkovic, R.A.Lerner, E.D.Getzoff, and J.A.Tainer (1990).
Antibody remodeling: a general solution to the design of a metal-coordination site in an antibody binding pocket.
  Proc Natl Acad Sci U S A, 87, 6654-6658.  
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SPKK, a new nucleic acid-binding unit of protein found in histone.
  EMBO J, 8, 797-804.  
2912725 W.Gebhard, M.Schube, and M.Eulitz (1989).
cDNA cloning and complete primary structure of the small, active subunit of human carboxypeptidase N (kininase 1).
  Eur J Biochem, 178, 603-607.  
3151020 A.E.Eriksson, P.M.Kylsten, T.A.Jones, and A.Liljas (1988).
Crystallographic studies of inhibitor binding sites in human carbonic anhydrase II: a pentacoordinated binding of the SCN- ion to the zinc at high pH.
  Proteins, 4, 283-293.
PDB codes: 2ca2 3ca2
3422451 G.Shoham, D.W.Christianson, and D.A.Oren (1988).
Complex between carboxypeptidase A and a hydrated ketomethylene substrate analogue.
  Proc Natl Acad Sci U S A, 85, 684-688.  
3416871 J.M.Sanchez-Ruiz, J.L.Lopez-Lacomba, P.L.Mateo, M.Vilanova, M.A.Serra, and F.X.Aviles (1988).
Analysis of the thermal unfolding of porcine procarboxypeptidase A and its functional pieces by differential scanning calorimetry.
  Eur J Biochem, 176, 225-230.  
3448607 H.Iijima, J.B.Dunbar, and G.R.Marshall (1987).
Calibration of effective van der Waals atomic contact radii for proteins and peptides.
  Proteins, 2, 330-339.  
3463986 D.W.Christianson, and W.N.Lipscomb (1986).
X-ray crystallographic investigation of substrate binding to carboxypeptidase A at subzero temperature.
  Proc Natl Acad Sci U S A, 83, 7568-7572.
PDB code: 3cpa
3455919 N.K.Honey, A.Y.Sakaguchi, P.A.Lalley, C.Quinto, W.J.Rutter, and S.L.Naylor (1986).
Assignment of the gene for carboxypeptidase A to human chromosome 7q22----qter and to mouse chromosome 6.
  Hum Genet, 72, 27-31.  
3863130 D.W.Christianson, and W.N.Lipscomb (1985).
Binding of a possible transition state analogue to the active site of carboxypeptidase A.
  Proc Natl Acad Sci U S A, 82, 6840-6844.  
3916340 K.D.Collins, and M.W.Washabaugh (1985).
The Hofmeister effect and the behaviour of water at interfaces.
  Q Rev Biophys, 18, 323-422.  
6595659 G.Shoham, D.C.Rees, and W.N.Lipscomb (1984).
Effects of pH on the structure and function of carboxypeptidase A: crystallographic studies.
  Proc Natl Acad Sci U S A, 81, 7767-7771.  
16593516 M.M.Teeter (1984).
Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin.
  Proc Natl Acad Sci U S A, 81, 6014-6018.
PDB code: 1crn
6580631 D.C.Rees, and W.N.Lipscomb (1983).
Crystallographic studies on apocarboxypeptidase A and the complex with glycyl-L-tyrosine.
  Proc Natl Acad Sci U S A, 80, 7151-7154.  
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