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(-) Description

Title :  X-RAY CRYSTALLOGRAPHIC INVESTIGATION OF SUBSTRATE BINDING TO CARBOXYPEPTIDASE A AT SUBZERO TEMPERATURE
 
Authors :  W. N. Lipscomb
Date :  24 Mar 82  (Deposition) - 29 Jul 82  (Release) - 25 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (C-Terminal Peptidase) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. W. Christianson, W. N. Lipscomb
X-Ray Crystallographic Investigation Of Substrate Binding To Carboxypeptidase A At Subzero Temperature.
Proc. Natl. Acad. Sci. Usa V. 83 7568 1986
PubMed-ID: 3463986  |  Reference-DOI: 10.1073/PNAS.83.20.7568
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE A
    Chains: A
    EC Number: 3.4.17.1
    Engineered: YES
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913
    Tissue: PANCREAS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GLY1Mod. Amino AcidGLYCINE
2TYR1Mod. Amino AcidTYROSINE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , SER A:197 , GLU A:270 , ZN A:308 , TYR A:502BINDING SITE FOR RESIDUE GLY A 501
2AC2SOFTWAREHIS A:69 , ASN A:144 , ARG A:145 , ILE A:243 , TYR A:248 , ALA A:250 , GLY A:253 , SER A:254 , ASP A:256 , GLU A:270 , GLY A:501BINDING SITE FOR RESIDUE TYR A 502
3AC3SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , GLY A:501BINDING SITE FOR RESIDUE ZN A 308

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:138 -A:161

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:197 -Tyr A:198
2Pro A:205 -Tyr A:206
3Arg A:272 -Asp A:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CBPA1_BOVIN_001 *I289VCBPA1_BOVIN  ---  ---AI179V
2UniProtVAR_CBPA1_BOVIN_002 *E338ACBPA1_BOVIN  ---  ---AA228A
3UniProtVAR_CBPA1_BOVIN_003 *L415VCBPA1_BOVIN  ---  ---AV305V
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPA1_BOVIN170-192  1A:60-82
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPA1_BOVIN306-316  1A:196-206

(-) Exons   (0, 0)

(no "Exon" information available for 3CPA)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:309
 aligned with CBPA1_BOVIN | P00730 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:309
                                   120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410         
          CBPA1_BOVIN   111 ARSTNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVEALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTLNNLY 419
               SCOP domains d3cpaa_ A: Carboxypeptidase A                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3cpaA00 A:1-307 Zn peptidases                                                                                                                                                                                                                                                                                      -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhh...eeeee............eeeee......eeeeeee.....hhhhhhhhhhhhhhhhh.....hhhhhhhhhheeeeee..hhhhhhhhhhh..................................................hhhhhhhhhhhhhhh..eeeeeee...eeeee..........hhhhhhhhhhhhhhhhh.......eee............hhhhhhhhh..eeeeeee.............hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------A----------------------------------------------------------------------------V---- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------CARBOXYPEPT_ZN_1       -----------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cpa A   1 ARSTNTFNYATYHTLDEIYDFMDLLVAQHPELVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTENYGQNPSFTAILDSMDIFLEIVTNPNGFAFTHSENRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKNHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVAALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTVNNGY 502
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300      || 
                                                                                                                                                                                                                                                                                                                                            307| 
                                                                                                                                                                                                                                                                                                                                             501
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CPA)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPA1_BOVIN | P00730)
molecular function
    GO:0004180    carboxypeptidase activity    Catalysis of the hydrolysis of the terminal or penultimate peptide bond at the C-terminal end of a peptide or polypeptide.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004181    metallocarboxypeptidase activity    Catalysis of the hydrolysis of C-terminal amino acid residues from a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CBPA1_BOVIN | P00730: 1arl 1arm 1bav 1cbx 1cps 1cpx 1ee3 1ell 1elm 1f57 1hdq 1hdu 1hee 1iy7 1m4l 1pyt 1yme 1zlh 2abz 2ctb 2ctc 2rfh 3fvl 3fx6 3i1u 3kgq 4cpa 5cpa 6cpa 7cpa 8cpa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3CPA)