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(-) Description

Title :  CRYSTAL STRUCTURE OF NITRILE HYDRATASE MUTANT BR56K COMPLEXED WITH TRIMETHYLACETONITRILE, PHOTO-ACTIVATED FOR 25 MIN
 
Authors :  Y. Yamanaka, K. Hashimoto, N. Noguchi, M. Yohda, M. Odaka
Date :  03 Dec 14  (Deposition) - 27 Jan 16  (Release) - 27 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.18
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydratase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yamanaka, Y. Kato, K. Hashimoto, K. Iida, K. Nagasawa, H. Nakayama, N. Dohmae, K. Noguchi, T. Noguchi, M. Yohda, M. Odaka
Time-Resolved Crystallography Of The Reaction Intermediate Of Nitrile Hydratase: Revealing A Role For The Cysteinesulfenic Acid Ligand As A Catalytic Nucleophile.
Angew. Chem. Int. Ed. Engl. V. 54 10763 2015
PubMed-ID: 26333053  |  Reference-DOI: 10.1002/ANIE.201502731

(-) Compounds

Molecule 1 - NITRILE HYDRATASE SUBUNIT ALPHA
    Chains: A
    EC Number: 4.2.1.84
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NTHA
    Organism Scientific: RHODOCOCCUS ERYTHROPOLIS
    Organism Taxid: 1833
    Synonym: NHASE, NITRILASE
 
Molecule 2 - NITRILE HYDRATASE SUBUNIT BETA
    Chains: B
    EC Number: 4.2.1.84
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NHA2, NTHB
    Mutation: YES
    Organism Scientific: RHODOCOCCUS ERYTHROPOLIS
    Organism Taxid: 1833
    Synonym: NHASE, NITRILASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2CSD1Mod. Amino Acid3-SULFINOALANINE
3CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
4FE1Ligand/IonFE (III) ION
5MG2Ligand/IonMAGNESIUM ION
6TAN1Ligand/Ion2,2-DIMETHYLPROPANENITRILE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:109 , CSD A:112 , SER A:113 , CSO A:114 , TAN A:302BINDING SITE FOR RESIDUE FE A 301
2AC2SOFTWAREGLN A:90 , CSD A:112 , SER A:113 , CSO A:114 , TRP A:117 , FE A:301BINDING SITE FOR RESIDUE TAN A 302
3AC3SOFTWARESER A:19 , TRP A:23 , GLU B:31 , TRP B:32BINDING SITE FOR RESIDUE CL A 304
4AC4SOFTWARETHR A:125 , TRP A:126 , HOH B:488 , HOH B:534 , HOH B:568BINDING SITE FOR RESIDUE CL A 305
5AC5SOFTWAREHOH B:403BINDING SITE FOR RESIDUE MG B 301
6AC6SOFTWAREGLU B:134 , TYR B:135 , SER B:192 , HOH B:610BINDING SITE FOR RESIDUE CL B 302
7AC7SOFTWARETHR B:121 , ARG B:132 , LEU B:208BINDING SITE FOR RESIDUE CL B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3X20)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3X20)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3X20)

(-) Exons   (0, 0)

(no "Exon" information available for 3X20)

(-) 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
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 3x20 A   9 ENAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLcScTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPT 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
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................hhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...........................eeee...........hhhhh..eeeeeee......hhhhhh..........eeeeeeehhhhhh......eeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3x20 B   1 MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVKYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPAA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
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  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 3X20)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3X20)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3X20)

(-) Gene Ontology  (7, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        NHAA_RHOER | P13448: 1ahj 2ahj 2cyz 2cz0 2cz1 2cz6 2cz7 2d0q 2qdy 2zcf 2zpb 2zpe 2zpf 2zpg 2zph 2zpi 3a8g 3a8h 3a8l 3a8m 3a8o 3wvd 3wve 3x24 3x25 3x26 3x28
        NHAB_RHOER | P13449: 1ahj 2ahj 2cyz 2cz0 2cz1 2cz6 2cz7 2d0q 2qdy 2zcf 2zpb 2zpe 2zpf 2zpg 2zph 2zpi 3a8g 3a8h 3a8l 3a8m 3a8o 3wvd 3wve 3x24 3x25 3x26 3x28

(-) Related Entries Specified in the PDB File

3wvd 3wve