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(-) Description

Title :  CRYSTAL STRUCTURE OF CO-TYPE NITRILE HYDRATASE FROM PSEUDONOCARDIA THERMOPHILA
 
Authors :  A. Miyanaga, S. Fushinobu, K. Ito, T. Wakagi
Date :  01 Oct 01  (Deposition) - 01 Oct 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Cysteine-Sulfinic Acid, Cysteine-Sulfenic Acid, Post-Translational Modification, Non-Corrin Cobalt, Nitrile, Hydration, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Miyanaga, S. Fushinobu, K. Ito, T. Wakagi
Crystal Structure Of Cobalt-Containing Nitrile Hydratase.
Biochem. Biophys. Res. Commun. V. 288 1169 2001
PubMed-ID: 11700034  |  Reference-DOI: 10.1006/BBRC.2001.5897
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NITRILE HYDRATASE
    ChainsA
    EC Number4.2.1.84
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC18
    Expression System StrainHB101
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificPSEUDONOCARDIA THERMOPHILA
    Organism Taxid1848
 
Molecule 2 - NITRILE HYDRATASE
    ChainsB
    EC Number4.2.1.84
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPUC18
    Expression System StrainHB101
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificPSEUDONOCARDIA THERMOPHILA
    Organism Taxid1848

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CO1Ligand/IonCOBALT (II) ION
2CSD1Mod. Amino Acid3-SULFINOALANINE
3CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2CSD2Mod. Amino Acid3-SULFINOALANINE
3CSO2Mod. Amino AcidS-HYDROXYCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:108 , CSD A:111 , SER A:112 , CSO A:113 , HOH A:432BINDING SITE FOR RESIDUE CO A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IRE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1IRE)

(-) Sequences/Alignments

Asymmetric 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:203
 aligned with NHAA_PSETH | Q7SID2 from UniProtKB/Swiss-Prot  Length:204

    Alignment length:203
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   
           NHAA_PSETH     2 TENILRKSDEEIQKEITARVKALESMLIEQGILTTSMIDRMAEIYENEVGPHLGAKVVVKAWTDPEFKKRLLADGTEACKELGIGGLQGEDMMWVENTDEVHHVVVCTLCSCYPWPVLGLPPNWFKEPQYRSRVVREPRQLLKEEFGFEVPPSKEIKVWDSSSEMRFVVLPQRPAGTDGWSEEELATLVTRESMIGVEPAKAV 204
               SCOP domains d1irea_ A: Cobalt-containing nitrile hydratase                                                                                                                                                              SCOP domains
               CATH domains 1ireA00 A:2-204 Nitrile Hydratase; Chain A                                                                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee....eeeeee.......hhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhh.......eeeeee....eeeeee..........hhhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ire A   2 TENILRKSDEEIQKEITARVKALESMLIEQGILTTSMIDRMAEIYENEVGPHLGAKVVVKAWTDPEFKKRLLADGTEACKELGIGGLQGEDMMWVENTDEVHHVVVCTLcScYPWPVLGLPPNWFKEPQYRSRVVREPRQLLKEEFGFEVPPSKEIKVWDSSSEMRFVVLPQRPAGTDGWSEEELATLVTRESMIGVEPAKAV 204
                                    11        21        31        41        51        61        71        81        91       101       111 |     121       131       141       151       161       171       181       191       201   
                                                                                                                                       111-CSD                                                                                         
                                                                                                                                         113-CSO                                                                                       

Chain B from PDB  Type:PROTEIN  Length:228
 aligned with NHAB_PSETH | Q7SID3 from UniProtKB/Swiss-Prot  Length:233

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
           NHAB_PSETH     1 MNGVYDVGGTDGLGPINRPADEPVFRAEWEKVAFAMFPATFRAGFMGLDEFRFGIEQMNPAEYLESPYYWHWIRTYIHHGVRTGKIDLEELERRTQYYRENPDAPLPEHEQKPELIEFVNQAVYGGLPASREVDRPPKFKEGDVVRFSTASPKGHARRARYVRGKTGTVVKHHGAYIYPDTAGNGLGECPEHLYTVRFTAQELWGPEGDPNSSVYYDCWEPYIELVDT 228
               SCOP domains d1ireb_ B: Cobalt-containing nitrile hydratase                                                                                                                                                                                       SCOP domains
               CATH domains 1ireB01 B:1-126  [code=1.10.472.20, no name defined]                                                                          ---1ireB02 B:130-228  [code=2.30.30.50, no name defined]                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh...ee............eeee...........hhhhh..eeeeeeeeeee.hhhhhh.......eeeeeeeeehhhhhhhhh...eeeeeeee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ire B   1 MNGVYDVGGTDGLGPINRPADEPVFRAEWEKVAFAMFPATFRAGFMGLDEFRFGIEQMNPAEYLESPYYWHWIRTYIHHGVRTGKIDLEELERRTQYYRENPDAPLPEHEQKPELIEFVNQAVYGGLPASREVDRPPKFKEGDVVRFSTASPKGHARRARYVRGKTGTVVKHHGAYIYPDTAGNGLGECPEHLYTVRFTAQELWGPEGDPNSSVYYDCWEPYIELVDT 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        

   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 Unit

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (NHAA_PSETH | Q7SID2)
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:0050897    cobalt ion binding    Interacting selectively and non-covalently with a cobalt (Co) ion.
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0050899    nitrile catabolic process    The chemical reactions and pathways resulting in the breakdown of a nitrile, an organic compound containing trivalent nitrogen attached to one carbon atom.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Chain B   (NHAB_PSETH | Q7SID3)
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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0050899    nitrile catabolic process    The chemical reactions and pathways resulting in the breakdown of a nitrile, an organic compound containing trivalent nitrogen attached to one carbon atom.
    GO:0006807    nitrogen compound metabolic process    The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NHAA_PSETH | Q7SID21ugp 1ugq 1ugr 1ugs 3vyh 4ob0 4ob1 4ob2 4ob3
        NHAB_PSETH | Q7SID31ugp 1ugq 1ugr 1ugs 3vyh 4ob0 4ob1 4ob2 4ob3

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