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(-) Description

Title :  CRYSTAL STRUCTURE OF FERVIDOLYSIN FROM FERVIDOBACTERIUM PENNIVORANS, A KERATINOLYTIC ENZYME RELATED TO SUBTILISIN
 
Authors :  J. S. Kim, L. D. Kluskens, W. M. De Vos, R. Huber, J. Van Der Oost
Date :  17 Oct 03  (Deposition) - 19 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Subtilisin, Sandwich Domain, Propeptide, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Kim, L. D. Kluskens, W. M. De Vos, R. Huber, J. Van Der Oost
Crystal Structure Of Fervidolysin From Fervidobacterium Pennivorans, A Keratinolytic Enzyme Related To Subtilisin.
J. Mol. Biol. V. 335 787 2004
PubMed-ID: 14687574  |  Reference-DOI: 10.1016/J.JMB.2003.11.006
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUBTILISIN-LIKE SERINE PROTEASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET9D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: PEPTIDASE
    Mutation: YES
    Organism Scientific: FERVIDOBACTERIUM PENNIVORANS
    Organism Taxid: 93466

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:137 , ASP A:179 , LYS A:219 , ASP A:221 , LYS A:223 , ILE A:225BINDING SITE FOR RESIDUE CA A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R6V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:314 -Pro A:315
2Gly A:447 -Pro A:448

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R6V)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUBTILASE_ASPPS00136 Serine proteases, subtilase family, aspartic acid active site.FLS_FERPE186-197  1A:166-177
2SUBTILASE_HISPS00137 Serine proteases, subtilase family, histidine active site.FLS_FERPE228-238  1A:209-218
3SUBTILASE_SERPS00138 Serine proteases, subtilase family, serine active site.FLS_FERPE407-417  1A:387-397

(-) Exons   (0, 0)

(no "Exon" information available for 1R6V)

(-) 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:671
 aligned with FLS_FERPE | Q93LQ6 from UniProtKB/Swiss-Prot  Length:699

    Alignment length:671
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698 
            FLS_FERPE    29 SKAKDLASLPEIKSQGYHILFGELRDGEYTEGKILVGYNDRSEVDKIVKAVNGKVVLELPQIKVVSIKLNGMTVKQAYDKIKALALKGIRYVEPSYKRELIKPTVVKPNPDMYKIRKPGLNSTARDYGEELSNELWGLEAIGVTQQLWEEASGTNIIVAVVDTGVDGTHPDLEGQVIAGYRPAFDEELPAGTDSSYGGSHGTHVAGTIAAKKDGKGIVGVAPGAKIMPIVIFDDPALVGGNGYVGDDYVAAGIIWATDHGAKVMNHSWGGWGYSYTMKEAFDYAMEHGVVMVVSAGNNTSDSHHQYPAGYPGVIQVAALDYYGGTFRVAGFSSRSDGVSVGAPGVTILSTVPGEDSIGYEGHNENVPATNGGTYDYYQGTSMAAPHVTGVVAVLLQKFPNAKPWQIRKLLENTAFDFNGNGWDHDTGYGLVKLDAALQGPLPTQGGVEEFQVVVTDAKGNFGVPTVFVSMMRDNGSCYYAKTGPDGIARFPHIDSGTYDIFVGGPDHWDRALAPYDGESIPGGYAIALRMAEERQASFVGFGVSPDATQLNVNFNSTLQVKFSTNLSTLKDPQFVVVDPLLRGVYGRVAYARNQTYDLSLLSGQISFGIQTLLPAATDITIQGTVTLNGEDIPVYGVLKAGTTWTIIDDFGGLNLGTDSQPIYVWWTIFGQ 699
               SCOP domains d1r6va_ A: Fervidolysin                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------1r6vA02 A:27-104  [code=3.30.70.80, no name defined]                          1r6vA03 A:105-451  [code=3.40.50.200, no name defined]                                                                                                                                                                                                                                                                                                     1r6vA04 A:452-563 Immunoglobulins                                                                               -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................eeeeee.hhhhhhhhhhhhh.eeeeeehhh.eeeee....hhhhhhhhhh......eeeee.....ee...ee.........................hhhhhhhhhhh..hhhhhhhh.....eeeeee......hhhhh.....eeehhhheee..........hhhhhhhhhhhh..............eeeeee...hhhhhh.....hhhhhhhhhhhhhhh...eeee.ee....hhhhhhhhhhhhhh..eeeee...................eeeeeeeee..eeee.........eeeeee...eeee.......................eeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.................hhhhhhhh......eeeeeeeeee..........eeeeee......eeee.....eeeeeeee.eeeeeeeeee.......................hhhhh.eeeeeeeee.....eeeee....eeeee..........eeeee......eeeeee.....eee....eeeeeeeee........eeeeeeeee..eeeeeeeee.....eeee..................eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_AS------------------------------SUBTILASE_H------------------------------------------------------------------------------------------------------------------------------------------------------------------------SUBTILASE_S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r6v A   9 SKAKDLASLPEIKSQGYHILFGELRDGEYTEGKILVGYNDRSEVDKIVKAVNGKVVLELPQIKVVSIKLNGMTVKQAYDKIKALALKGIRYVEPSYKRELIKPTVVKPNPDMYKIRKPGLNSTARDYGEELSNELWGLEAIGVTQQLWEEASGTNIIVAVVDTGVDGTHPDLEGQVIAGYRPAFDEELPAGTDSSYGGSAGTHVAGTIAAKKDGKGIVGVAPGAKIMPIVIFDDPALVGGNGYVGDDYVAAGIIWATDHGAKVMNHSWGGWGYSYTMKEAFDYAMEHGVVMVVSAGNNTSDSHHQYPAGYPGVIQVAALDYYGGTFRVAGFSSRSDGVSVGAPGVTILSTVPGEDSIGYEGHNENVPATNGGTYDYYQGTSMAAPHVTGVVAVLLQKFPNAKPWQIRKLLENTAFDFNGNGWDHDTGYGLVKLDAALQGPLPTQGGVEEFQVVVTDAKGNFGVPTVFVSMMRDNGSCYYAKTGPDGIARFPHIDSGTYDIFVGGPDHWDRALAPYDGESIPGGYAIALRMAEERQASFVGFGVSPDATQLNVNFNSTLQVKFSTNLSTLKDPQFVVVDPLLRGVYGRVAYARNQTYDLSLLSGQISFGIQTLLPAATDITIQGTVTLNGEDIPVYGVLKAGTTWTIIDDFGGLNLGTDSQPIYVWWTIFGQ 679
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678
   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) (23833)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1R6V)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (FLS_FERPE | Q93LQ6)
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: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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  1r6v
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 Related Entries

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