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(-) Description

Title :  CRYSTAL STRUCTURE OF A TAIWAN HABU VENOM METALLOPROTEINASE COMPLEXED WITH PEQW.
 
Authors :  K. F. Huang, S. H. Chiou, T. P. Ko, A. H. J. Wang
Date :  22 Jan 02  (Deposition) - 10 Jul 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Protein, Retro-Binding Manner, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. F. Huang, S. H. Chiou, T. P. Ko, A. H. Wang
Determinants Of The Inhibition Of A Taiwan Habu Venom Metalloproteinase By Its Endogenous Inhibitors Revealed By X-Ray Crystallography And Synthetic Inhibitor Analogues.
Eur. J. Biochem. V. 269 3047 2002
PubMed-ID: 12071970  |  Reference-DOI: 10.1046/J.1432-1033.2002.02982.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METALLOPROTEINASE
    Chains: A
    EC Number: 3.4.24.44
    Fragment: CATALYTIC PROTEASE DOMAIN
    Organism Scientific: PROTOBOTHROPS MUCROSQUAMATUS
    Organism Taxid: 103944
    Synonym: ATROLYSIN E
 
Molecule 2 - EQW
    Chains: B
    Engineered: YES
    Other Details: PEQW WAS SYNTHESIZED BY SOLID-PHASE CHEMICAL METHOD.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1CD10Ligand/IonCADMIUM ION
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:144 , HIS A:148 , HIS A:154 , HOH B:414BINDING SITE FOR RESIDUE CD A 801
02AC2SOFTWAREHIS A:36 , ASP A:156 , ASP A:158 , HOH A:349 , HOH A:350BINDING SITE FOR RESIDUE CD A 802
03AC3SOFTWAREASP A:181 , ASP A:185 , HOH A:326 , HOH A:432 , HOH A:434BINDING SITE FOR RESIDUE CD A 803
04AC4SOFTWAREHIS A:18 , HOH A:467 , HOH A:592BINDING SITE FOR RESIDUE CD A 804
05AC5SOFTWAREGLN A:7 , ASN A:50 , HOH A:320 , HOH A:321 , HOH A:439 , HOH A:441BINDING SITE FOR RESIDUE CD A 805
06AC6SOFTWAREASP A:194 , HOH A:443 , HOH A:500 , HOH A:578 , HOH A:600BINDING SITE FOR RESIDUE CD A 806
07AC7SOFTWAREPRO A:203 , HOH A:393 , HOH A:625BINDING SITE FOR RESIDUE CD A 807
08AC8SOFTWAREHIS A:131 , HOH A:355 , HOH A:356 , HOH A:357 , HOH A:425BINDING SITE FOR RESIDUE CD A 808
09AC9SOFTWAREHOH A:381 , HOH A:387 , HOH A:555 , HOH A:556 , HOH A:557BINDING SITE FOR RESIDUE CD A 809
10BC1SOFTWAREGLU A:85 , HOH A:455 , HOH A:456BINDING SITE FOR RESIDUE CD A 810

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:119 -A:198
2A:160 -A:182
3A:162 -A:165

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADAM_MEPROPS50215 ADAM type metalloprotease domain profile.VM2T3_PROMU197-392  1A:8-203
2ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.VM2T3_PROMU330-339  1A:141-150

(-) Exons   (0, 0)

(no "Exon" information available for 1KUI)

(-) 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:201
 aligned with VM2T3_PROMU | O57413 from UniProtKB/Swiss-Prot  Length:481

    Alignment length:201
                                   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
          VM2T3_PROMU   192 QRFPQRYIKLAIVVDHGMYTKYSSNFKKIRKRVHQMVSNINEMCRPLNIAITLALLDVWSEKDFITVQADAPTTAGLFGDWRERVLLKKKNHDHAQLLTDTNFARNTIGWAYVGRMCDEKYSVAVVKDHSSKVFMVAVTMTHELGHNLGMEHDDKDKCKCDTCIMSAVISDKQSKLFSDCSKDYYQTFLTNDNPQCILNAP 392
               SCOP domains d1kuia_ A: Snake venom metalloprotease                                                                                                                                                                    SCOP domains
               CATH domains 1kuiA00 A:3-203 Collagenase (Catalytic Domain)                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeehhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee...........hhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.eee...........eeeee....hhhhhhhhhhhhhhhhh.............................hhhhhhhhhhhhhhh.hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----ADAM_MEPRO  PDB: A:8-203 UniProt: 197-392                                                                                                                                                            PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE----------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kui A   3 QRFPQRYIELAIVVDHGMYTKYSSNFKKIRKRVHQMVSNINEMCRPLNIAITLALLDVWSEKDFITVQADAPTTAGLFGDWRERVLLKKKNHDHAQLLTDTNFARNTIGWAYVGRMCDEKYSVAVVKDHSSKVFMVAVTMTHELGHNLGMEHDDKDKCKCDTCIMSAVISDKQSKLFSDCSKDYYQTFLTNDNPQCILNAP 203
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 


Chain B from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 1kui B 251 xQW 253
                            |  
                          251-PCA
   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  (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 1KUI)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VM2T3_PROMU | O57413)
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: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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  1kui
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  VM2T3_PROMU | O57413
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  3.4.24.44
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 Related Entries

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

UniProtKB/Swiss-Prot
        VM2T3_PROMU | O57413: 1kuf 1kug 1kuk

(-) Related Entries Specified in the PDB File

1kuf 1KUF CONTAINS THE SAME METALLOPROTEINASE WITHOUT INHIBITOR BINDING
1kug 1KUG CONTAINS THE SAME PROTEIN COMPLEXED WITH ITS ENDOGENOUS INHIBITOR PENW.
1kuk 1KUK CONTAINS THE SAME PROTEIN COMPLEXED WITH PEKW.