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(-) Description

Title :  CRYSTAL STRUCTURE OF CO-TYPE NITRILE HYDRATASE BETA-E56Q FROM PSEUDOMONAS PUTIDA.
 
Authors :  H. R. Brodkin, W. R. P. Novak, D. Ringe, G. A. Petsko
Date :  03 Mar 11  (Deposition) - 23 Mar 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Nitrile Hydratase, Co, Cobalt, Cysteine Sulfinic Acid, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. R. Brodkin, W. R. Novak, A. C. Milne, J. A. D'Aquino, N. M. Karabacak, I. G. Goldberg, J. N. Agar, M. S. Payne, G. A. Petsko, M. J. Ondrechen, D. Ringe
Evidence Of The Participation Of Remote Residues In The Catalytic Activity Of Co-Type Nitrile Hydratase From Pseudomonas Putida.
Biochemistry V. 50 4923 2011
PubMed-ID: 21473592  |  Reference-DOI: 10.1021/BI101761E

(-) Compounds

Molecule 1 - CO-TYPE NITRILE HYDRATASE ALPHA SUBUNIT
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303
 
Molecule 2 - CO-TYPE NITRILE HYDRATASE BETA SUBUNIT
    Chains: B, D, F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PSEUDOMONAS PUTIDA
    Organism Taxid: 303

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
13CO4Ligand/IonCOBALT (III) ION
2CSD8Mod. Amino Acid3-SULFINOALANINE
3GOL4Ligand/IonGLYCEROL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
13CO1Ligand/IonCOBALT (III) ION
2CSD2Mod. Amino Acid3-SULFINOALANINE
3GOL1Ligand/IonGLYCEROL
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
13CO1Ligand/IonCOBALT (III) ION
2CSD2Mod. Amino Acid3-SULFINOALANINE
3GOL1Ligand/IonGLYCEROL
Biological Unit 3 (3, 4)
No.NameCountTypeFull Name
13CO1Ligand/IonCOBALT (III) ION
2CSD2Mod. Amino Acid3-SULFINOALANINE
3GOL1Ligand/IonGLYCEROL
Biological Unit 4 (3, 4)
No.NameCountTypeFull Name
13CO1Ligand/IonCOBALT (III) ION
2CSD2Mod. Amino Acid3-SULFINOALANINE
3GOL1Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:11 , GLN A:15 , LYS A:131 , ALA A:133 , HOH A:255 , TYR B:63 , LEU B:64 , GLY B:66BINDING SITE FOR RESIDUE GOL A 212
2AC2SOFTWARECYS A:112 , CSD A:115 , SER A:116 , CSD A:117BINDING SITE FOR RESIDUE 3CO A 213
3AC3SOFTWAREHIS C:11 , GLY C:13 , GLN C:15 , ALA C:132 , ALA C:133 , LEU D:64 , GLY D:66 , TYR D:68BINDING SITE FOR RESIDUE GOL C 212
4AC4SOFTWARECYS C:112 , CSD C:115 , SER C:116 , CSD C:117BINDING SITE FOR RESIDUE 3CO C 213
5AC5SOFTWAREHIS E:11 , GLN E:15 , ALA E:132 , ALA E:133 , TYR F:63 , LEU F:64 , GLY F:66BINDING SITE FOR RESIDUE GOL E 212
6AC6SOFTWARECYS E:112 , CSD E:115 , SER E:116 , CSD E:117 , HOH E:1049BINDING SITE FOR RESIDUE 3CO E 213
7AC7SOFTWAREHIS G:11 , GLN G:15 , ALA G:132 , ALA G:133 , LEU H:64 , GLY H:66 , THR H:67 , TYR H:68BINDING SITE FOR RESIDUE GOL G 212
8AC8SOFTWARECYS G:112 , CSD G:115 , SER G:116 , CSD G:117BINDING SITE FOR RESIDUE 3CO G 213

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QYG)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3QYG)

(-) 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:201
                                                                                                                                                                                                                                         
               SCOP domains d3qyga_ A: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee....eeeeee.......hhhhhh..hhhhhhhhhhhhhh.hhhhhhhhh........eeeeee.....eeeee..........hhhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyg A   7 HDHHHDGYQAPPEDIALRVKALESLLIEKGLVDPAAMDLVVQTYEHKVGPRNGAKVVAKAWVDPAYKARLLADGTAGIAELGFSGVQGEDMVILENTPAVHNVFVCTLcScYPWPTLGLPPAWYKAAPYRSRMVSDPRGVLAEFGLVIPANKEIRVWDTTAELRYMVLPERPAGTEAYSEEQLAELVTRDSMIGTGLPTQP 207
                                    16        26        36        46        56        66        76        86        96       106       116|      126       136       146       156       166       176       186       196       206 
                                                                                                                                      115-CSD                                                                                        
                                                                                                                                        117-CSD                                                                                      


Chain B from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3qygb_ B: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh............hhhhhhhhhhhh.................eeee...........hhhhh..eeeeeeeeeee.hhhhhh.......eeeeeeeeehhhhhh........eeeeeee...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyg B   1 MNGIHDTGGAHGYGPVYREPNEPVFRYDWEKTVMSLLPALLANGNFNLDEFRHSIQRMGPAHYLEGTYYEHWLHVFENLLVEKGVLTATEVATGKAASGKTATPVLTPAIVDGLLSTGASAAREEGARARFAVGDKVRVLNKNPVGHTRMPRYTRGKVGTVVIDHGVFVTPDTAAHGKGEHPQHVYTVSFTSVELWGQDASSPKDTIRVDLWDDYLEPA 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain C from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains d3qygc_ C: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee....eeeeee.......hhhhhh..hhhhhhhhhhhhhh.hhhhhhhhh........eeeeee.....eeeee..........hhhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyg C   7 HDHHHDGYQAPPEDIALRVKALESLLIEKGLVDPAAMDLVVQTYEHKVGPRNGAKVVAKAWVDPAYKARLLADGTAGIAELGFSGVQGEDMVILENTPAVHNVFVCTLcScYPWPTLGLPPAWYKAAPYRSRMVSDPRGVLAEFGLVIPANKEIRVWDTTAELRYMVLPERPAGTEAYSEEQLAELVTRDSMIGTGLPTQP 207
                                    16        26        36        46        56        66        76        86        96       106       116|      126       136       146       156       166       176       186       196       206 
                                                                                                                                      115-CSD                                                                                        
                                                                                                                                        117-CSD                                                                                      


Chain D from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3qygd_ D: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh............hhhhhhhhhhhh.................eeee...........hhhhh..eeeeeeeeeee.hhhhhh.......eeeeeeeeehhhhhh........eeeeeee...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyg D   1 MNGIHDTGGAHGYGPVYREPNEPVFRYDWEKTVMSLLPALLANGNFNLDEFRHSIQRMGPAHYLEGTYYEHWLHVFENLLVEKGVLTATEVATGKAASGKTATPVLTPAIVDGLLSTGASAAREEGARARFAVGDKVRVLNKNPVGHTRMPRYTRGKVGTVVIDHGVFVTPDTAAHGKGEHPQHVYTVSFTSVELWGQDASSPKDTIRVDLWDDYLEPA 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain E from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains d3qyge_ E: automated matches                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee....eeeeee.......hhhhhh..hhhhhhhhhhhhhh.hhhhhhhhh........eeeeee.....eeeee..........hhhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyg E   8 DHHHDGYQAPPEDIALRVKALESLLIEKGLVDPAAMDLVVQTYEHKVGPRNGAKVVAKAWVDPAYKARLLADGTAGIAELGFSGVQGEDMVILENTPAVHNVFVCTLcScYPWPTLGLPPAWYKAAPYRSRMVSDPRGVLAEFGLVIPANKEIRVWDTTAELRYMVLPERPAGTEAYSEEQLAELVTRDSMIGTGLPTQP 207
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
                                                                                                                                     115-CSD                                                                                        
                                                                                                                                       117-CSD                                                                                      


Chain F from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3qygf_ F: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh............hhhhhhhhhhhh.................eeee...........hhhhh..eeeeeeeeeee.hhhhhh.......eeeeeeeeehhhhhh........eeeeeee...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyg F   1 MNGIHDTGGAHGYGPVYREPNEPVFRYDWEKTVMSLLPALLANGNFNLDEFRHSIQRMGPAHYLEGTYYEHWLHVFENLLVEKGVLTATEVATGKAASGKTATPVLTPAIVDGLLSTGASAAREEGARARFAVGDKVRVLNKNPVGHTRMPRYTRGKVGTVVIDHGVFVTPDTAAHGKGEHPQHVYTVSFTSVELWGQDASSPKDTIRVDLWDDYLEPA 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain G from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains d3qygg_ G: automated matches                                                                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeee....eeeeee.......hhhhhh.......hhhhhhhhh.hhhhhhhhh........eeeeee.....eeeee..........hhhhhhh..hhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyg G   8 DHHHDGYQAPPEDIALRVKALESLLIEKGLVDPAAMDLVVQTYEHKVGPRNGAKVVAKAWVDPAYKARLLADGTAGIAELGFSGVQGEDMVILENTPAVHNVFVCTLcScYPWPTLGLPPAWYKAAPYRSRMVSDPRGVLAEFGLVIPANKEIRVWDTTAELRYMVLPERPAGTEAYSEEQLAELVTRDSMIGTGLPTQP 207
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
                                                                                                                                     115-CSD                                                                                        
                                                                                                                                       117-CSD                                                                                      


Chain H from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains d3qygh_ H: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh............hhhhhhhhhhhh.................eeee...........hhhhh..eeeeeeeeeee.hhhhhh.......eeeeeeeeehhhhhh........eeeeeee...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qyg H   1 MNGIHDTGGAHGYGPVYREPNEPVFRYDWEKTVMSLLPALLANGNFNLDEFRHSIQRMGPAHYLEGTYYEHWLHVFENLLVEKGVLTATEVATGKAASGKTATPVLTPAIVDGLLSTGASAAREEGARARFAVGDKVRVLNKNPVGHTRMPRYTRGKVGTVVIDHGVFVTPDTAAHGKGEHPQHVYTVSFTSVELWGQDASSPKDTIRVDLWDDYLEPA 219
                                    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)
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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  (2, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3QYG)

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  3qyg
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 Related Entries

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(-) Related Entries Specified in the PDB File

3qxe 3qyh 3qz5 3qz9