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(-) Description

Title :  CRYSTAL STRUCTURE OF PHOTO-ACTIVATION STATE OF NITRILE HYDRATASE MUTANT S113A
 
Authors :  Y. Yamanaka, K. Hashimoto, A. Ohtaki, K. Noguchi, M. Yohda, M. Odaka
Date :  06 Oct 09  (Deposition) - 14 Apr 10  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nitrile Hydratase, Fe, Iron, Lyase, Metal-Binding, Oxidation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Yamanaka, K. Hashimoto, A. Ohtaki, K. Noguchi, M. Yohda, M. Odaka
Kinetic And Structural Studies On Roles Of The Serine Ligan And A Strictly Conserved Tyrosine Residue In Nitrile Hydratase
J. Biol. Inorg. Chem. V. 15 655 2010
PubMed-ID: 20221653  |  Reference-DOI: 10.1007/S00775-010-0632-3

(-) Compounds

Molecule 1 - NITRILE HYDRATASE SUBUNIT ALPHA
    ChainsA
    EC Number4.2.1.84
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPRCN103
    Expression System Taxid562
    Expression System Vector TypePLASMID
    MutationYES
    Organism ScientificRHODOCOCCUS ERYTHROPOLIS
    Organism Taxid1833
    StrainN-771
    SynonymNITRILE HYDRATASE ALPHA-SUBUNIT, NITRILASE, NHASE
 
Molecule 2 - NITRILE HYDRATASE SUBUNIT BETA
    ChainsB
    EC Number4.2.1.84
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHSGB
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificRHODOCOCCUS ERYTHROPOLIS
    Organism Taxid1833
    StrainN-771
    SynonymNITRILE HYDRATASE BETA-SUBUNIT, NITRILASE, NHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1CSD1Mod. Amino Acid3-SULFINOALANINE
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3FE1Ligand/IonFE (III) ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:109 , CSD A:112 , ALA A:113 , CSO A:114 , HOH A:613BINDING SITE FOR RESIDUE FE A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A8L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3A8L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_NHAB_RHOER_001 *M40VNHAB_RHOER  ---  ---BM40V
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3A8L)

(-) Exons   (0, 0)

(no "Exon" information available for 3A8L)

(-) 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:197
 aligned with NHAA_RHOER | P13448 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:197
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       
           NHAA_RHOER    10 ENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLCSCTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPT 206
               SCOP domains d3a8la_ A: automated matches                                                                                                                                                                          SCOP domains
               CATH domains 3a8lA00 A:9-205 Nitrile Hydratase; Chain A                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee....eeeeee.......hhhhhh..hhhhhhhhhhhhh..hhhhhhhhhh.......eeeeee.....eeeee..........hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8l A   9 ENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLcAcTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPT 205
                                    18        28        38        48        58        68        78        88        98       108   | | 118       128       138       148       158       168       178       188       198       
                                                                                                                                 112-CSD                                                                                         
                                                                                                                                   114-CSO                                                                                       

Chain B from PDB  Type:PROTEIN  Length:212
 aligned with NHAB_RHOER | P13449 from UniProtKB/Swiss-Prot  Length:212

    Alignment length:212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  
           NHAB_RHOER     1 MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVRYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPAA 212
               SCOP domains d3a8lb_ B: Iron-containing nitrile hydratase                                                                                                                                                                         SCOP domains
               CATH domains 3a8lB01 B:1-110  [code=1.10.472.20, no name defined]                                                          3a8lB02 B:111-212  [code=2.30.30.50, no name defined]                                                  CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................hhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhh.hhhhhhhhhhhhhhhhh...hhhhhhhhhh...........................eeee...........hhhhh..eeeeeee......hhhhhh..........eeeeeeehhhhhh......eeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a8l B   1 MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVRYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPAA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210  

   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  (2, 2)

Asymmetric/Biological Unit

(-) 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 3A8L)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NHAA_RHOER | P13448)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0080109    indole-3-acetonitrile nitrile hydratase activity    Catalysis of the reaction: indole-3-acetonitrile + H2O = indole-3-acetamide.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0018822    nitrile hydratase activity    Catalysis of the reaction: an aliphatic amide = a nitrile + H2O.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

Chain B   (NHAB_RHOER | P13449)
molecular function
    GO:0080109    indole-3-acetonitrile nitrile hydratase activity    Catalysis of the reaction: indole-3-acetonitrile + H2O = indole-3-acetamide.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0018822    nitrile hydratase activity    Catalysis of the reaction: an aliphatic amide = a nitrile + H2O.
    GO:0046914    transition metal ion binding    Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NHAA_RHOER | P134481ahj 2ahj 2cyz 2cz0 2cz1 2cz6 2cz7 2d0q 2qdy 2zcf 2zpb 2zpe 2zpf 2zpg 2zph 2zpi 3a8g 3a8h 3a8m 3a8o 3wvd 3wve 3x20 3x24 3x25 3x26 3x28
        NHAB_RHOER | P134491ahj 2ahj 2cyz 2cz0 2cz1 2cz6 2cz7 2d0q 2qdy 2zcf 2zpb 2zpe 2zpf 2zpg 2zph 2zpi 3a8g 3a8h 3a8m 3a8o 3wvd 3wve 3x20 3x24 3x25 3x26 3x28

(-) Related Entries Specified in the PDB File

3a8g 3a8h 3a8m 3a8o