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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN THE LEECH CARBOXYPEPTIDASE INHIBITOR AND THE HUMAN CARBOXYPEPTIDASE A2 (LCI-CPA2)
 
Authors :  D. Reverter, C. Fernandez-Catalan, W. Bode, T. A. Holak, F. X. Aviles
Date :  12 Jan 00  (Deposition) - 12 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Carboxypeptidase A2, Leech Carboxypeptidase Inhibitor, Hydrolase/Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Reverter, C. Fernandez-Catalan, R. Baumgartner, R. Pfander, R. Huber, W. Bode, J. Vendrell, T. A. Holak, F. X. Aviles
Structure Of A Novel Leech Carboxypeptidase Inhibitor Determined Free In Solution And In Complex With Human Carboxypeptidase A2.
Nat. Struct. Biol. V. 7 322 2000
PubMed-ID: 10742178  |  Reference-DOI: 10.1038/74092
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CARBOXYPEPTIDASE A2
    ChainsA
    EC Number3.4.15.1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - METALLOCARBOXYPEPTIDASE INHIBITOR
    ChainsB
    Organism CommonMEDICINAL LEECH
    Organism ScientificHIRUDO MEDICINALIS
    Organism Taxid6421

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GLU1Mod. Amino AcidGLUTAMIC ACID
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:300 , HIS A:424 , GLU A:427 , HIS A:552 , VAL B:66BINDING SITE FOR RESIDUE ZN A 301
2AC2SOFTWAREHOH A:49 , HOH A:254 , ZN A:301 , HIS A:424 , ARG A:482 , ASN A:500 , ARG A:501 , HIS A:552 , TYR A:604 , ALA A:606 , GLU A:626 , VAL B:66BINDING SITE FOR RESIDUE GLU A 300

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:494 -A:517
2A:566 -A:600
3B:11 -B:34
4B:18 -B:62
5B:19 -B:43
6B:22 -B:58

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DTD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1DTD)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CARBOXYPEPT_ZN_1PS00132 Zinc carboxypeptidases, zinc-binding region 1 signature.CBPA2_HUMAN170-192  1A:415-437
2CARBOXYPEPT_ZN_2PS00133 Zinc carboxypeptidases, zinc-binding region 2 signature.CBPA2_HUMAN306-316  1A:552-562

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002224811aENSE00001871689chr7:129906667-129906792126CBPA2_HUMAN1-24240--
1.2ENST000002224812ENSE00000723205chr7:129908769-12990885082CBPA2_HUMAN24-51280--
1.3ENST000002224813ENSE00000364674chr7:129909509-129909643135CBPA2_HUMAN52-96450--
1.4ENST000002224814ENSE00000723214chr7:129910533-12991062896CBPA2_HUMAN97-128321A:363-37311
1.5aENST000002224815aENSE00000723216chr7:129912916-129913017102CBPA2_HUMAN129-162341A:374-40734
1.7ENST000002224817ENSE00001729197chr7:129914989-12991508799CBPA2_HUMAN163-195331A:408-44033
1.8aENST000002224818aENSE00001790144chr7:129916468-129916578111CBPA2_HUMAN196-232371A:441-47737
1.9ENST000002224819ENSE00000723221chr7:129917666-12991775691CBPA2_HUMAN233-263311A:478-50932
1.10ENST0000022248110ENSE00000723222chr7:129919303-129919502200CBPA2_HUMAN263-329671A:509-57567
1.11ENST0000022248111ENSE00000723223chr7:129921944-12992202885CBPA2_HUMAN330-358291A:576-60429
1.12ENST0000022248112ENSE00001930985chr7:129929400-129929638239CBPA2_HUMAN358-419621A:604-66562

(-) 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:303
 aligned with CBPA2_HUMAN | P48052 from UniProtKB/Swiss-Prot  Length:419

    Alignment length:303
                                                                                                                                                          245                                                                                                                                                                              
                                                                                                                                                        244 |                                                                                                                                                                              
                                   127       137       147       157       167       177       187       197       207       217       227       237      |246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416   
          CBPA2_HUMAN   118 FNFGAYHTLEEISQEMDNLVAEHPGLVSKVNIGSSFENRPMNVLKFSTGGDKPAIWLDAGIHAREWVTQATALWTANKIVSDYGKDPSITSILDALDIFLLPVTNPDGYVFSQTKNRMWRKTRSKVS-GSLCVGVDPNRNWDAGFGGPGASSNPCSDSYHGPSANSEVEVKSIVDFIKSHGKVKAFITLHSYSQLLMFPYGYKCTKLDDFDELSEVAQKAAQSLRSLHGTKYKVGPICSVIYQASGGSIDWSYDYGIKYSFAFELRDTGRYGFLLPARQILPTAEETWLGLKAIMEHVRDHPY 419
               SCOP domains d1dtda_ A: Carboxypeptidase A                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh...eeeeeeee.....eeeeeee.......eeeee......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhheeeee...hhhhhhhhhhh....................hhhhh..........................hhhhhhhhhhhhhhh.eeeeeeee....eeee..................................eeeehhhhh.....hhhhhhhhhh..eeeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------CARBOXYPEPT_ZN_1       ------------------------------------------------------------------------------------------------------------------CARBOXYPEPT------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4   Exon 1.5a  PDB: A:374-407         Exon 1.7  PDB: A:408-440         Exon 1.8a  PDB: A:441-477            -------------------------------Exon 1.10  PDB: A:509-575 UniProt: 263-329                         Exon 1.11  PDB: A:576-604    ------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:478-509        ----------------------------------------------------------------------------------------------Exon 1.12  PDB: A:604-665 UniProt: 358-419                     Transcript 1 (2)
                 1dtd A 363 FNFGAYHTLEEISQEMDNLVAEHPGLVSKVNIGSSFENRPMNVLKFSTGGDKPAIWLDAGIHAREWVTQATALWTANKIVSDYGKDPSITSILDALDIFLLPVTNPDGYVFSQTKNRMWRKTRSKVSAGSLCVGVDPNRNWDAGFGGPGASSNPCSDSYHGPSANSEVEVKSIVDFIKSHGKVKAFIILHSYSQLLMFPYGYKCTKLDDFDELSEVAQKAAQSLSRLHGTKYKVGPICSVIYQASGGSIDWSYDYGIKYSFAFELRDTGRYGFLLPARQILPTAEETWLGLKAIMEHVRDHPY 665
                                   372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662   

Chain B from PDB  Type:PROTEIN  Length:61
 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 d1dtdb_ B: Carboxypeptidase inhibitor                         SCOP domains
               CATH domains 1dtdB00 B:6-66  [code=3.30.1040.10, no name defined]          CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....eeeeeee....hhhhheeee...hhhhhhhh...eee..eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 1dtd B   6 DESFLCYQPDQVCCFICRGAAPLPSEGECNPHPTAPWCREGAVEWVPYSTGQCRTTCIPYV  66
                                    15        25        35        45        55        65 

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1DTD)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CBPA2_HUMAN | P48052)
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:0007039    protein catabolic process in the vacuole    The chemical reactions and pathways resulting in the breakdown of a protein in the vacuole, usually by the action of vacuolar proteases.
    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.
    GO:0005773    vacuole    A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

Chain B   (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
        CBPA2_HUMAN | P480521aye 1o6x
        MCPI_HIRME | P815111dtv 1zfi 1zfl 2abz

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