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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HYDROGENASE 3 MATURATION PROTEASE
 
Authors :  T. Tanaka, T. S. Kumarevel, A. Shinkai, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  18 Jan 07  (Deposition) - 22 Jan 08  (Release) - 06 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrogenase, Maturation, Protease, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kumarevel, T. Tanaka, Y. Bessho, A. Shinkai, S. Yokoyama
Crystal Structure Of Hydrogenase Maturating Endopeptidase Hyci From Escherichia Coli
Biochem. Biophys. Res. Commun. V. 389 310 2009
PubMed-ID: 19720045  |  Reference-DOI: 10.1016/J.BBRC.2009.08.135
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYDROGENASE 3 MATURATION PROTEASE
    Chains: A, B
    EC Number: 3.4.-.-
    Engineered: YES
    Expression System: CELL-FREE SYNTHESIS
    Expression System Plasmid: PCA24N
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:39 , ALA A:42 , ASN A:45 , ASP A:46 , HOH A:1010 , HOH A:1018BINDING SITE FOR RESIDUE CA A 1002
2AC2SOFTWAREASP A:116 , HOH A:1015 , HOH A:1043 , HOH A:1061 , HOH A:1062 , HOH A:1068BINDING SITE FOR RESIDUE CA A 1003
3AC3SOFTWAREGLY B:39 , ALA B:42 , ASN B:45 , ASP B:46 , HOH B:1008 , HOH B:1010BINDING SITE FOR RESIDUE CA B 1001
4AC4SOFTWAREASP B:16 , ASP B:62 , ALA B:63 , HOH B:1047 , HOH B:1080 , HOH B:1094BINDING SITE FOR RESIDUE CA B 1004
5AC5SOFTWAREASP A:99 , HOH A:1063 , HOH A:1064 , GLN B:100 , GLU B:103 , HOH B:1017 , HOH B:1051 , HOH B:1079BINDING SITE FOR RESIDUE CA B 1005
6AC6SOFTWAREGLY A:32 , GLU A:140 , GLU B:140 , HOH B:1033 , HOH B:1035 , HOH B:1040 , HOH B:1072 , HOH B:1097BINDING SITE FOR RESIDUE CA B 1006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E85)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E85)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E85)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E85)

(-) Exons   (0, 0)

(no "Exon" information available for 2E85)

(-) 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:156
 aligned with HYCI_ECOLI | P0AEV9 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:156
                               1                                                                                                                                                        
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      
           HYCI_ECOLI     - ---MTDVLLCVGNSMMGDDGAGPLLAEKCAAAPKGNWVVIDGGSAPENDIVAIRELRPTRLLIVDATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQLKEDIGEVIFLGIQPDIVGFYYPMTQPIKDAVETVYQRLEGWEGNGGFAQLAV 153
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee.hhhhhhhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh..eeeeeee.........eee.hhhhhhhh........hhhhhhhhhhhhhheeeeeee...........hhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2e85 A  -2 ASAVTDVLLCVGNSMMGDDGAGPLLAEKCAAAPKGNWVVIDGGSAPENDIVAIRELRPTRLLIVDATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQLKEDIGEVIFLGIQPDIVGFYYPMTQPIKDAVETVYQRLEGWEGNGGFAQLAV 153
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147      


Chain B from PDB  Type:PROTEIN  Length:157
 aligned with HYCI_ECOLI | P0AEV9 from UniProtKB/Swiss-Prot  Length:156

    Alignment length:157
                               1                                                                                                                                                         
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       
           HYCI_ECOLI     - ---MTDVLLCVGNSMMGDDGAGPLLAEKCAAAPKGNWVVIDGGSAPENDIVAIRELRPTRLLIVDATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQLKEDIGEVIFLGIQPDIVGFYYPMTQPIKDAVETVYQRLEGWEGNGGFAQLAVE 154
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhhhhhhhhhhh.....eeeeee..hhhhhhhhhhhh..eeeeeee.........eee.hhhhhhhh........hhhhhhhhhhhhhh.eeeeee...........hhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e85 B  -2 ASAVTDVLLCVGNSMMGDDGAGPLLAEKCAAAPKGNWVVIDGGSAPENDIVAIRELRPTRLLIVDATDMGLNPGEIRIIDPDDIAEMFMMTTHNMPLNYLIDQLKEDIGEVIFLGIQPDIVGFYYPMTQPIKDAVETVYQRLEGWEGNGGFAQLAVE 154
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147
   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  (0, 0)

(no "SCOP Domain" information available for 2E85)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2E85)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E85)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HYCI_ECOLI | P0AEV9)
molecular function
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    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: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:0043085    positive regulation of catalytic activity    Any process that activates or increases the activity of an enzyme.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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UniProtKB/Swiss-Prot
        HYCI_ECOLI | P0AEV9: 2i8l

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