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(-) Description

Title :  CRYSTAL STRUCTURE OF C19A/C43A MUTANT OF LEECH CARBOXYPEPTIDASE INHIBITOR IN COMPLEX WITH BOVINE CARBOXYPEPTIDASE A
 
Authors :  J. L. Arolas, G. M. Popowicz, S. Bronsoms, F. X. Aviles, R. Huber, T. A. Holak, S. Ventura
Date :  18 Jul 05  (Deposition) - 31 Jan 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Inhibitor-Metallocarboxypeptidase Complex, Lci Mutant, Oxidative Folding Intermediate Analog, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. L. Arolas, G. M. Popowicz, S. Bronsoms, F. X. Aviles, R. Huber, T. A. Holak, S. Ventura
Study Of A Major Intermediate In The Oxidative Folding Of Leech Carboxypeptidase Inhibitor: Contribution Of The Fourth Disulfide Bond
J. Mol. Biol. V. 352 961 2005
PubMed-ID: 16126224  |  Reference-DOI: 10.1016/J.JMB.2005.07.065
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE A1
    ChainsA, B
    EC Number3.4.17.1
    EngineeredYES
    Expression SystemPICHIA PASTORIS
    Expression System PlasmidPPIC9
    Expression System StrainKM71
    Expression System Taxid4922
    Expression System Vector TypePLASMID
    Organism CommonCATTLE
    Organism ScientificBOS TAURUS
    Organism Taxid9913
    SynonymCARBOXYPEPTIDASE A, CPA, A/B METALLOCARBOXYPEPTIDASE
 
Molecule 2 - METALLOCARBOXYPEPTIDASE INHIBITOR
    ChainsC, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPBAT4
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonMEDICINAL LEECH
    Organism ScientificHIRUDO MEDICINALIS
    Organism Taxid6421
    SynonymLEECH CARBOXYPEPTIDASE INHIBITOR, LCI, INHIBITOR OF A/B METALLOCARBOXYPEPTIDASES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , GLU A:72 , HIS A:196 , VAL C:66BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREHIS B:69 , GLU B:72 , HIS B:196 , VAL E:66BINDING SITE FOR RESIDUE ZN B 1002

(-) SS Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1A:138 -A:161
2B:138 -B:161
3C:11 -C:34
4C:18 -C:62
5C:22 -C:58
6D:11 -D:34
7D:18 -D:58
8D:22 -D:62
9E:11 -E:34
10E:18 -E:62
11E:22 -E:58
12F:11 -F:34
13F:18 -F:62
14F:22 -F:58

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Ser A:197 -Tyr A:198
2Pro A:205 -Tyr A:206
3Arg A:272 -Asp A:273
4Ser B:197 -Tyr B:198
5Pro B:205 -Tyr B:206
6Arg B:272 -Asp B:273
7Cys D:62 -Ile D:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_CBPA1_BOVIN_001 *I289VCBPA1_BOVIN  ---  ---A/BI179V
2UniProtVAR_CBPA1_BOVIN_002 *E338ACBPA1_BOVIN  ---  ---A/BA228A
3UniProtVAR_CBPA1_BOVIN_003 *L415VCBPA1_BOVIN  ---  ---A/BV305V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPA1_BOVIN170-192
 
  2A:60-82
B:60-82
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPA1_BOVIN306-316
 
  2A:196-206
B:196-206

(-) Exons   (0, 0)

(no "Exon" information available for 2ABZ)

(-) 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:299
 aligned with CBPA1_BOVIN | P00730 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:302
                                   123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413  
          CBPA1_BOVIN   114 TNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVEALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTL 415
               SCOP domains d2abza_ A: Carboxypeptidase A                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 2abzA00 A:4-305 Zn peptidases                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh..........---.....................................hhhhhhhhhhhhhhh.eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhh......eeeehhhhh.....hhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------A----------------------------------------------------------------------------V SAPs(SNPs)
                    PROSITE --------------------------------------------------------CARBOXYPEPT_ZN_1       -----------------------------------------------------------------------------------------------------------------CARBOXYPEPT--------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2abz A   4 TNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSV---SLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVAALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTV 305
                                    13        23        33        43        53        63        73        83        93       103       113       123        |-  |    143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303  
                                                                                                                                                          132 136                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:301
 aligned with CBPA1_BOVIN | P00730 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:303
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412   
          CBPA1_BOVIN   113 STNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSVTSSSLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVEALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTL 415
               SCOP domains d2abzb_ B: Carboxypeptidase A                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 2abzB00 B:3-305 Zn peptidases                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee........eeeeee.....hhhhhhhhhhhhhhhhhhh..hhhhhhhhh..eeeee...hhhhhhhhhhh...........--.....................................hhhhhhhhhhhhhhh.eeeeeeee....eeee..........hhhhhhhhhhhhhhhhhhh.....eeeehhhhh.....hhhhhhhhh...eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V------------------------------------------------A----------------------------------------------------------------------------V SAPs(SNPs)
                    PROSITE ---------------------------------------------------------CARBOXYPEPT_ZN_1       -----------------------------------------------------------------------------------------------------------------CARBOXYPEPT--------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2abz B   3 STNTFNYATYHTLDEIYDFMDLLVAEHPQLVSKLQIGRSYEGRPIYVLKFSTGGSNRPAIWIDLGIHSREWITQATGVWFAKKFTEDYGQDPSFTAILDSMDIFLEIVTNPDGFAFTHSQNRLWRKTRSVT--SLCVGVDANRNWDAGFGKAGASSSPCSETYHGKYANSEVEVKSIVDFVKDHGNFKAFLSIHSYSQLLLYPYGYTTQSIPDKTELNQVAKSAVAALKSLYGTSYKYGSIITTIYQASGGSIDWSYNQGIKYSFTFELRDTGRYGFLLPASQIIPTAQETWLGVLTIMEHTV 305
                                    12        22        32        42        52        62        72        82        92       102       112       122       132|  |   142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302   
                                                                                                                                                            133  |                                                                                                                                                                         
                                                                                                                                                               136                                                                                                                                                                         

Chain C from PDB  Type:PROTEIN  Length:62
 aligned with MCPI_HIRME | P81511 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:62
                                    28        38        48        58        68        78  
           MCPI_HIRME    19 PDESFLCYQPDQVCCFICRGAAPLPSEGECNPHPTAPWCREGAVEWVPYSTGQCRTTCIPYV  80
               SCOP domains d2abzc1 C:5-66 Carboxypeptidase inhibitor                      SCOP domains
               CATH domains 2abzC00 C:5-66  [code=3.30.1040.10, no name defined]           CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeeeee....hhhhheeee...hhhhhhhh...eee..eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 2abz C   5 PDESFLCYQPDQVCAFICRGAAPLPSEGECNPHPTAPWAREGAVEWVPYSTGQCRTTCIPYV  66
                                    14        24        34        44        54        64  

Chain D from PDB  Type:PROTEIN  Length:46
 aligned with MCPI_HIRME | P81511 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:60
                                    27        37        47        57        67        77
           MCPI_HIRME    18 TPDESFLCYQPDQVCCFICRGAAPLPSEGECNPHPTAPWCREGAVEWVPYSTGQCRTTCI  77
               SCOP domains d2abzd_ D  : au tomated ma tches                             SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee--.eee-eee.......-..eeee.......----------..ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 2abz D   4 TPDESFLCY--DQVC-FICRGAAPLP-EGECNPHPTAPWA----------STGQCRTTCI  63
                                    |- |  | | 23     | |33        43         -|       63
                                   12 15 18 |       29 |          43         54         
                                           20         31                                

Chain E from PDB  Type:PROTEIN  Length:60
 aligned with MCPI_HIRME | P81511 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:61
                                    29        39        49        59        69        79 
           MCPI_HIRME    20 DESFLCYQPDQVCCFICRGAAPLPSEGECNPHPTAPWCREGAVEWVPYSTGQCRTTCIPYV  80
               SCOP domains d2abze_ E: automated matches                                  SCOP domains
               CATH domains 2abzE00 E:6-66  [code=3.30.1040.10, no name defi ned]         CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeeeee....hhhhheeee...hhhhhhhh...ee.-..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 2abz E   6 DESFLCYQPDQVCAFICRGAAPLPSEGECNPHPTAPWAREGAVEWVPY-TGQCRTTCIPYV  66
                                    15        25        35        45       |55        65 
                                                                          53 |           
                                                                            55           

Chain F from PDB  Type:PROTEIN  Length:58
 aligned with MCPI_HIRME | P81511 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:63
                                    27        37        47        57        67        77   
           MCPI_HIRME    18 TPDESFLCYQPDQVCCFICRGAAPLPSEGECNPHPTAPWCREGAVEWVPYSTGQCRTTCIPYV  80
               SCOP domains d2abzf_ F: automated matches                                    SCOP domains
               CATH domains 2abzF00 F:4-66  [code=3.30.1040.10, no na   me de  fined]       CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee....hhhhheeee........---.....--..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 2abz F   4 TPDESFLCYQPDQVCAFICRGAAPLPSEGECNPHPTAPWAR---VEWVP--TGQCRTTCIPYV  66
                                    13        23        33        43|   |   |- |      63   
                                                                   44  48  52 55           

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ABZ)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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.

Chain C,D,E,F   (MCPI_HIRME | P81511)
molecular function
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
    GO:0008191    metalloendopeptidase inhibitor activity    Stops, prevents or reduces the activity of metalloendopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain and contain a chelated metal ion at their active sites which is essential to their catalytic activity.
    GO:0030414    peptidase inhibitor activity    Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
biological process
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010466    negative regulation of peptidase activity    Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBPA1_BOVIN | P007301arl 1arm 1bav 1cbx 1cps 1cpx 1ee3 1ell 1elm 1f57 1hdq 1hdu 1hee 1iy7 1m4l 1pyt 1yme 1zlh 2ctb 2ctc 2rfh 3cpa 3fvl 3fx6 3i1u 3kgq 4cpa 5cpa 6cpa 7cpa 8cpa
        MCPI_HIRME | P815111dtd 1dtv 1zfi 1zfl

(-) Related Entries Specified in the PDB File

1dtd CRYSTAL STRUCTURE OF THE LEECH CARBOXYPEPTIDASE INHIBITOR IN COMPLEX WITH HUMAN CARBOXYPEPTIDASE A2
1dtv SOLUTION STRUCTURE OF THE LEECH CARBOXYPEPTIDASE INHIBITOR DETERMINED AT PH 6.5
1zfl SOLUTION STRUCTURE OF III-A, THE MAJOR INTERMEDIATE IN THE OXIDATIVE FOLDING OF LEECH CARBOXYPEPTIDASE INHIBITOR