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(-) Description

Title :  STRUCTURAL OF ABDH, A BETA-DIKETONE HYDROLASE FROM THE CYANOBACTERIUM ANABAENA SP. PCC 7120 BOUND TO (S)-3-OXOCYCLOHEXYL ACETIC ACID
 
Authors :  J. P. Bennett, J. L. Whittingham, A. M. Brzozowski, P. M. Leonard, G. Grogan
Date :  19 Sep 06  (Deposition) - 08 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Enzyme Evolution, C-C Bond Hydrolase, Hydrolase, Lyase, Crotonase, Biocatalysis, Beta-Diketone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Bennett, J. L. Whittingham, A. M. Brzozowski, P. M. Leonard, G. Grogan
Structural Characterisation Of A Beta Diketone Hydrolase From The Cyanobacterium Anabaena Sp. Pcc 7120 In Native And Product Bound Forms, A Coenzyme A-Independent Member Of The Crotonase Suprafamily
Biochemistry V. 46 137 2007
PubMed-ID: 17198383  |  Reference-DOI: 10.1021/BI061900G

(-) Compounds

Molecule 1 - BETA-DIKETONE HYDROLASE
    Chains: A, B
    EC Number: 3.7.1.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: ANABAENA SP.
    Organism Taxid: 103690
    Other Details: PROTEIN WAS CO-CRYSTALLISED WITH SUBSTRATE
    Strain: PCC 7120

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1KTA2Ligand/Ion(S)-CYCLOHEXANONE-2-ACETATE
2NI2Ligand/IonNICKEL (II) ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1KTA6Ligand/Ion(S)-CYCLOHEXANONE-2-ACETATE
2NI-1Ligand/IonNICKEL (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:2221 , HOH A:2222 , HOH A:2224BINDING SITE FOR RESIDUE NI A1254
2AC2SOFTWAREHOH B:2219 , HOH B:2221 , HOH B:2222BINDING SITE FOR RESIDUE NI B1254
3AC3SOFTWAREPHE A:38 , HIS A:43 , PHE A:77 , HIS A:121 , PRO A:143 , HOH A:2051 , HOH A:2247BINDING SITE FOR RESIDUE KTA A1253
4AC4SOFTWAREPHE B:38 , PHE B:77 , LEU B:80 , TRP B:89 , HIS B:121 , PRO B:143 , ILE B:149 , HOH B:2061 , HOH B:2235BINDING SITE FOR RESIDUE KTA B1253

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2J5S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J5S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J5S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2J5S)

(-) Exons   (0, 0)

(no "Exon" information available for 2J5S)

(-) 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:251
 aligned with Q8YNV6_NOSS1 | Q8YNV6 from UniProtKB/TrEMBL  Length:253

    Alignment length:251
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252 
         Q8YNV6_NOSS1     3 LNQPEYFTKYENLHFHRDENGILEVRMHTNGSSLVFTGKTHREFPDAFYDISRDRDNRVVILTGSGDAWMAEIDFPSLGDVTNPREWDKTYWEGKKVLQNLLDIEVPVISAVNGAALLHSEYILTTDIILASENTVFQDMPHLNAGIVPGDGVHILWPLALGLYRGRYFLFTQEKLTAQQAYELNVVHEVLPQSKLMERAWEIARTLAKQPTLNLRYTRVALTQRLKRLVNEGIGYGLALEGITATDLRNT 253
               SCOP domains d2j5sa_ A: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains 2j5sA00 A:3-253 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhh...eeeee....eeeeee.......eehhhhhhhhhhhhhhhhhh....eeeee....eee.ee.hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee..ee..hhhhhhhh.eeeee...ee..hhhhhhh.....hhhhhhhhhhh.hhhhhhhhh...eehhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j5s A   3 LNQPEYFTKYENLHFHRDENGILEVRMHTNGSSLVFTGKTHREFPDAFYDISRDRDNRVVILTGSGDAWMAEIDFPSLGDVTNPREWDKTYWEGKKVLQNLLDIEVPVISAVNGAALLHSEYILTTDIILASENTVFQDMPHLNAGIVPGDGVHILWPLALGLYRGRYFLFTQEKLTAQQAYELNVVHEVLPQSKLMERAWEIARTLAKQPTLNLRYTRVALTQRLKRLVNEGIGYGLALEGITATDLRNT 253
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252 


Chain B from PDB  Type:PROTEIN  Length:249
 aligned with Q8YNV6_NOSS1 | Q8YNV6 from UniProtKB/TrEMBL  Length:253

    Alignment length:249
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244         
         Q8YNV6_NOSS1     5 QPEYFTKYENLHFHRDENGILEVRMHTNGSSLVFTGKTHREFPDAFYDISRDRDNRVVILTGSGDAWMAEIDFPSLGDVTNPREWDKTYWEGKKVLQNLLDIEVPVISAVNGAALLHSEYILTTDIILASENTVFQDMPHLNAGIVPGDGVHILWPLALGLYRGRYFLFTQEKLTAQQAYELNVVHEVLPQSKLMERAWEIARTLAKQPTLNLRYTRVALTQRLKRLVNEGIGYGLALEGITATDLRNT 253
               SCOP domains d2j5sb_ B: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains 2j5sB00 B:5-253 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...eeeee....eeeeee.......eehhhhhhhhhhhhhhhhhh....eeeee....eee.ee.hhhhh...hhhhhhhhhhhhhhhhhhhhh....eeeee..ee..hhhhhhhh.eeeee...ee..hhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eehhhhhhh....eeehhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2j5s B   5 QPEYFTKYENLHFHRDENGILEVRMHTNGSSLVFTGKTHREFPDAFYDISRDRDNRVVILTGSGDAWMAEIDFPSLGDVTNPREWDKTYWEGKKVLQNLLDIEVPVISAVNGAALLHSEYILTTDIILASENTVFQDMPHLNAGIVPGDGVHILWPLALGLYRGRYFLFTQEKLTAQQAYELNVVHEVLPQSKLMERAWEIARTLAKQPTLNLRYTRVALTQRLKRLVNEGIGYGLALEGITATDLRNT 253
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J5S)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8YNV6_NOSS1 | Q8YNV6)
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.
biological process
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8YNV6_NOSS1 | Q8YNV6: 2j5g

(-) Related Entries Specified in the PDB File

2j5g THE NATIVE STRUCTURE OF A BETA-DIKETONE HYDROLASE FROM THE CYANOBACTERIUM ANABAENA SP. PCC 7120
2j5j STRUCTURAL OF ABDH, A BETA-DIKETONE HYDROLASE FROM THE CYANOBACTERIUM ANABAENA SP. PCC 7120 BOUND TO 3-PROPYL GLUTARIC ACID