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(-) Description

Title :  ZINC PEPTIDASE FROM GRIFOLA FRONDOSA
 
Authors :  T. Hori, T. Kumasaka, M. Yamamoto, T. Nonaka, N. Tanaka, Y. Hashimoto, T. Ueki, K. Takio
Date :  11 Oct 00  (Deposition) - 14 Mar 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Zinc Coordinate, Metalloprotease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Hori, T. Kumasaka, M. Yamamoto, N. Nonaka, N. Tanaka, Y. Hashimoto, U. Ueki, K. Takio
Structure Of A New 'Aspzincin' Metalloendopeptidase From Grifola Frondosa: Implications For The Catalytic Mechanism And Substrate Specificity Based On Several Different Crystal Forms.
Acta Crystallogr. , Sect. D V. 57 361 2001
PubMed-ID: 11223512  |  Reference-DOI: 10.1107/S0907444900019740
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDYL-LYS METALLOENDOPEPTIDASE
    Chains: A
    EC Number: 3.4.24.20
    Organism Scientific: GRIFOLA FRONDOSA
    Organism Taxid: 5627
    Tissue: FRUITING BODY

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:39 , THR A:42 , THR A:43 , HOH A:483BINDING SITE FOR RESIDUE MAN A 900
2AC2SOFTWAREHIS A:117 , HIS A:121 , ASP A:130 , HOH A:346 , HOH A:513BINDING SITE FOR RESIDUE ZN A 200

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:5 -A:75
2A:77 -A:97

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:163 -Pro A:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1GE6)

(-) Exons   (0, 0)

(no "Exon" information available for 1GE6)

(-) 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:163
 aligned with PLMP_GRIFR | P81054 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:163
                                   195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345   
           PLMP_GRIFR   186 CSSSEQSALAAAASAAQSYVAESLSYLQTHTAATPRYTTWFGSYISSRHSTVLQHYTDMNSNDFSSYSFDCTCTAAGTFAYVYPNRFGTVYLCGAFWKAPTTGTDSQAGTLVHESSHFTRNGGTKDYAYGQAAAKSLATMDPDKAVMNADNHEYFSENNPAQS 348
               SCOP domains d1ge6a_ A: Fungal zinc peptidase                                                                                                                                    SCOP domains
               CATH domains 1ge6A00 A:5-167 Collagenase (Catalytic Domain)                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhheee.........ee.......eeeehhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ge6 A   5 CSSSEQSALAAAASAAQSYVAESLSYLQTHTAATPRYTTWFGSYISSRHSTVLQHYTDMNSNDFSSYSFDCTCTAAGTFAYVYPNRFGTVYLCGAFWKAPTTGTDSQAGTLVHESSHFTRNGGTKDYAYGQAAAKSLATMDPDKAVMNADNHEYFSENNPAQS 167
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164
   Legend:   → Mismatch (orange background)
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  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 1GE6)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PLMP_GRIFR | P81054)
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.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        PLMP_GRIFR | P81054: 1g12 1ge5 1ge7

(-) Related Entries Specified in the PDB File

1g12 1G12 CONTAINS THE SAME ENZYME WITH DIFFERENT CRYSTAL FORM.
1ge5 1GE5 CONTAINS THE SAME ENZYME WITH DIFFERENT CRYSTAL FORM.
1ge7 1GE7 CONTAINS THE SAME ENZYME WITH DIFFERENT CRYSTAL FORM.