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(-) Description

Title :  HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE P-I SNAKE VENOM METALLOPROTEINASE BAP1 IN COMPLEX WITH A PEPTIDOMIMETIC: INSIGHTS INTO INHIBITOR BINDING
 
Authors :  T. J. Lingott, C. Schleberger, J. M. Gutierrez, I. Merfort
Date :  14 Oct 08  (Deposition) - 16 Jun 09  (Release) - 21 Sep 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.46
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase Inhibitor Complex, Metal-Binding, Zinc-Depending, Metalloprotease, Metalloproteinase/Inhibitor Complex, Zinc, Toxin, Secreted, Protease, Hydrolase, P-I Snake Venom Metalloproteinase, Metzincin, Chemotaxis, Adamalysin, Endopeptidase, Alpha-Beta Protein, Matrixmetalloproteinase, Tumor Necrosis Factor Alpha Converting Enzyme, Pyrrolidone Carboxylic Acid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Lingott, C. Schleberger, J. M. Gutierrez, I. Merfort
High-Resolution Crystal Structure Of The Snake Venom Metalloproteinase Bap1 Complexed With A Peptidomimetic: Insight Into Inhibitor Binding.
Biochemistry V. 48 6166 2009
PubMed-ID: 19485419  |  Reference-DOI: 10.1021/BI9002315
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC METALLOPROTEINASE BAP1
    Chains: A
    EC Number: 3.4.24.-
    Fragment: RESIDUES 193-394
    Organism Common: TERCIOPELO
    Organism Scientific: BOTHROPS ASPER
    Organism Taxid: 8722
    Secretion: VENOM
    Synonym: HEMORRHAGIC METALLOPROTEINASE BAP1, BAP-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 4)

Asymmetric/Biological Unit (4, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID
3WR21Ligand/Ion(2R,3R)-N^1^-[(1S)-2,2-DIMETHYL-1-(METHYLCARBAMOYL)PROPYL]-N^4^-HYDROXY-2-(2-METHYLPROPY-3-{[(1,3-THIAZOL-2-YLCARBONYL)AMINO]METHYL}BUTANEDIAMIDE
4ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:142 , HIS A:146 , HIS A:152 , WR2 A:1204BINDING SITE FOR RESIDUE ZN A 1203
2AC3SOFTWAREARG A:110 , ALA A:111 , GLU A:143 , HIS A:146 , LYS A:201 , PRO A:202 , WR2 A:1204 , HOH A:2266 , HOH A:2365BINDING SITE FOR RESIDUE GOL A 1205
3ZZZAUTHORASN A:106 , THR A:107 , ILE A:108 , GLY A:109 , ARG A:110 , THR A:139 , HIS A:142 , GLU A:143 , HIS A:146 , HIS A:152 , SER A:168 , VAL A:169 , LEU A:170BINDING SITE FOR RESIDUE WR2 A 1204

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:117 -A:197
2A:157 -A:181
3A:159 -A:164

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W12)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W12)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADAM_MEPROPS50215 ADAM type metalloprotease domain profile.VM1B1_BOTAS198-394  1A:6-202
2ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.VM1B1_BOTAS331-340  1A:139-148

(-) Exons   (0, 0)

(no "Exon" information available for 2W12)

(-) 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:202
 aligned with VM1B1_BOTAS | P83512 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:202
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392  
          VM1B1_BOTAS   193 QRFSPRYIELAVVADHGIFTKYNSNLNTIRTRVHEMLNTVNGFYRSVDVHAPLANLEVWSKQDLIKVQKDSSKTLKSFGEWRERDLLPRISHDHAQLLTAVVFDGNTIGRAYTGGMCDPRHSVGVVRDHSKNNLWVAVTMAHELGHNLGIHHDTGSCSCGAKSCIMASVLSKVLSYEFSDCSQNQYETYLTNHNPQCILNKP 394
               SCOP domains d2w12a_ A: Snake venom metalloprotease                                                                                                                                                                     SCOP domains
               CATH domains -2w12A00 A:2-202 Collagenase (Catalytic Domain)                                                                                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.......eeeeee...........hhhhhhhhhhhhhhhhhhhhh...eeeeee.........eee...........eeeee....hhhhhhhhhhhhhhhhh..............................hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----ADAM_MEPRO  PDB: A:6-202 UniProt: 198-394                                                                                                                                                             PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w12 A   1 xRFSPRYIELAVVADHGIFTKYNSNLNTIRTRVHEMLNTVNGFYRSVDVHAPLANLEVWSKQDLIKVQKDSSKTLKSFGEWRERDLLPRISHDHAQLLTAVVFDGNTIGRAYTGGMCDPRHSVGVVRDHSKNNLWVAVTMAHELGHNLGIHHDTGSCSCGAKSCIMASVLSKVLSYEFSDCSQNQYETYLTNHNPQCILNKP 202
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
                            |                                                                                                                                                                                                         
                            1-PCA
   Legend:   → Mismatch (orange background)
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  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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2W12)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VM1B1_BOTAS | P83512)
molecular function
    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:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in 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:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        VM1B1_BOTAS | P83512: 1nd1 2w13 2w14 2w15

(-) Related Entries Specified in the PDB File

1nd1 AMINO ACID SEQUENCE AND CRYSTAL STRUCTURE OF BAP1, AMETALLOPROTEINASE FROM BOTHROPS ASPER SNAKE VENOM THATEXERTS MULTIPLE TISSUE- DAMAGING ACTIVITIES.
2w13 HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE P- I SNAKE VENOM METALLOPROTEINASE BAP1 IN COMPLEX WITH A PEPTIDOMIMETIC: INSIGHTS INTO INHIBITOR BINDING
2w14 HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE P- I SNAKE HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE P-I SNAKE HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE P-I SNAKE
2w15 HIGH-RESOLUTION CRYSTAL STRUCTURE OF THE P- I SNAKE VENOM METALLOPROTEINASE BAP1 IN COMPLEX WITH A PEPTIDOMIMETIC: INSIGHTS INTO INHIBITOR BINDING