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(-) Description

Title :  HIGH-RESOLUTION CRYSTAL STRUCTURE OF A SNAKE VENOM METALLOPROTEINASE FROM TAIWAN HABU
 
Authors :  K. F. Huang, S. H. Chiou, T. P. Ko, J. M. Yuann, A. H. J. Wang
Date :  21 Jan 02  (Deposition) - 03 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Alpha/Beta Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. F. Huang, S. H. Chiou, T. P. Ko, J. M. Yuann, A. H. Wang
The 1. 35 A Structure Of Cadmium-Substituted Tm-3, A Snake-Venom Metalloproteinase From Taiwan Habu: Elucidation Of A Tnfalpha-Converting Enzyme-Like Active-Site Structure With A Distorted Octahedral Geometry Of Cadmium.
Acta Crystallogr. , Sect. D V. 58 1118 2002
PubMed-ID: 12077431  |  Reference-DOI: 10.1107/S090744490200656X
(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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1CD10Ligand/IonCADMIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:144 , HIS A:148 , HIS A:154 , HOH A:359 , HOH A:416 , HOH A:418BINDING SITE FOR RESIDUE CD A 701
02AC2SOFTWAREHIS A:36 , ASP A:156 , ASP A:158 , HOH A:350 , HOH A:351BINDING SITE FOR RESIDUE CD A 702
03AC3SOFTWAREASP A:181 , ASP A:185 , HOH A:327 , HOH A:435 , HOH A:437BINDING SITE FOR RESIDUE CD A 703
04AC4SOFTWAREHIS A:18 , HOH A:600 , HOH A:601 , HOH A:602 , HOH A:632 , HOH A:634BINDING SITE FOR RESIDUE CD A 704
05AC5SOFTWAREGLN A:7 , ASN A:50 , HOH A:320 , HOH A:321 , HOH A:404 , HOH A:442BINDING SITE FOR RESIDUE CD A 705
06AC6SOFTWAREASP A:194 , HOH A:447 , HOH A:448 , HOH A:533 , HOH A:586BINDING SITE FOR RESIDUE CD A 706
07AC7SOFTWAREPRO A:203 , HOH A:391 , HOH A:395 , HOH A:472BINDING SITE FOR RESIDUE CD A 707
08AC8SOFTWAREHIS A:131 , HOH A:356 , HOH A:357 , HOH A:358 , HOH A:428BINDING SITE FOR RESIDUE CD A 708
09AC9SOFTWAREHOH A:383 , HOH A:389 , HOH A:562 , HOH A:563 , HOH A:564BINDING SITE FOR RESIDUE CD A 709
10BC1SOFTWAREGLU A:85 , HOH A:458 , HOH A:459 , HOH A:460 , HOH A:595BINDING SITE FOR RESIDUE CD A 710

(-) 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 1KUF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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 1KUF)

(-) 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 d1kufa_ A: Snake venom metalloprotease                                                                                                                                                                    SCOP domains
               CATH domains 1kufA00 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.hhhhhh.. 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
                 1kuf A   3 QRFPQRYIELAIVVDHGMYTKYSSNFKKIRKRVHQMVSNINEMCRPLNIAITLALLDVWSEKDFITVQADAPTTAGLFGDWRERVLLKKKNHDHAQLLTDTNFARNTIGWAYVGRMCDEKYSVAVVKDHSSKVFMVAVTMTHELGHNLGMEHDDKDKCKCDTCIMSAVISDKQSKLFSDCSKDYYQTFLTNDNPQCILNAP 203
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
   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 1KUF)

(-) 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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  1kuf
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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: 1kug 1kui 1kuk

(-) Related Entries Specified in the PDB File

1kug 1KUG CONTAINS THE SAME PROTEIN COMPLEXED WITH ITS ENDOGENOUS INHIBITOR PENW.