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(-) Description

Title :  CRYSTAL STRUCTURE OF OMEGA-TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM
 
Authors :  C. Sayer, M. N. Isupov, J. A. Littlechild
Date :  11 Sep 12  (Deposition) - 27 Mar 13  (Release) - 03 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Sayer, M. N. Isupov, A. Westlake, J. A. Littlechild
Structural Studies With Pseudomonas And Chromobacterium [Omega]-Aminotransferases Provide Insights Into Their Differing Substrate Specificity.
Acta Crystallogr. , Sect. D V. 69 564 2013
PubMed-ID: 23519665  |  Reference-DOI: 10.1107/S0907444912051670

(-) Compounds

Molecule 1 - AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.18
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1PXG2Ligand/Ion3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:59 , TRP A:60 , SER A:119 , GLY A:120 , SER A:121 , TYR A:153 , HIS A:154 , GLY A:155 , GLU A:226 , ALA A:231 , ASP A:259 , VAL A:261 , ILE A:262 , ALA A:287 , ARG A:416 , HOH A:2025 , HOH A:2193 , HOH A:2233 , HOH A:2235 , HOH A:2305 , HOH A:2306 , HOH A:2307BINDING SITE FOR RESIDUE PXG A 470
2AC2SOFTWAREHOH A:2091 , LEU B:59 , TRP B:60 , SER B:119 , GLY B:120 , SER B:121 , TYR B:153 , HIS B:154 , GLY B:155 , GLU B:226 , ALA B:231 , ASP B:259 , VAL B:261 , ILE B:262 , ALA B:287 , ARG B:416 , HOH B:2075 , HOH B:2076 , HOH B:2161 , HOH B:2272 , HOH B:2273BINDING SITE FOR RESIDUE PXG B 470
3AC3SOFTWAREASN A:387 , THR B:196 , PRO B:197 , ASP B:198BINDING SITE FOR RESIDUE SO4 B1460

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4BA5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:175 -Pro A:176
2Leu B:175 -Pro B:176

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4BA5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4BA5)

(-) Exons   (0, 0)

(no "Exon" information available for 4BA5)

(-) 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:427
 aligned with Q7NWG4_CHRVO | Q7NWG4 from UniProtKB/TrEMBL  Length:459

    Alignment length:427
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       
         Q7NWG4_CHRVO    33 ARVMTRGEGVYLWDSEGNKIIDGMAGLWCVNVGYGRKDFAEAARRQMEELPFYNTFFKTTHPAVVELSSLLAEVTPAGFDRVFYTNSGSESVDTMIRMVRRYWDVQGKPEKKTLIGRWNGYHGSTIGGASLGGMKYMHEQGDLPIPGMAHIEQPWWYKHGKDMTPDEFGVVAARWLEEKILEIGADKVAAFVGEPIQGAGGVIVPPATYWPEIERICRKYDVLLVADEVICGFGRTGEWFGHQHFGFQPDLFTAAKGLSSGYLPIGAVFVGKRVAEGLIAGGDFNHGFTYSGHPVCAAVAHANVAALRDEGIVQRVKDDIGPYMQKRWRETFSRFEHVDDVRGVGMVQAFTLVKNKAKRELFPDFGEIGTLCRDIFFRNNLIMRACGDHIVSAPPLVMTRAEVDEMLAVAERCLEEFEQTLKARGLA 459
               SCOP domains d4ba5a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhh.hhhhhhh.......eeee...hhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh.....eeeeehhhhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeeeeee....ee....hhhhhhhhhhhhhh.ee.eee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ba5 A  33 ARVMTRGEGVYLWDSEGNKIIDGMAGLWCVNVGYGRKDFAEAARRQMEELPFYNTFFKTTHPAVVELSSLLAEVTPAGFDRVFYTNSGSESVDTMIRMVRRYWDVQGKPEKKTLIGRWNGYHGSTIGGASLGGMKYMHEQGDLPIPGMAHIEQPWWYKHGKDMTPDEFGVVAARWLEEKILEIGADKVAAFVGEPIQGAGGVIVPPATYWPEIERICRKYDVLLVADEVICGFGRTGEWFGHQHFGFQPDLFTAAKGLSSGYLPIGAVFVGKRVAEGLIAGGDFNHGFTYSGHPVCAAVAHANVAALRDEGIVQRVKDDIGPYMQKRWRETFSRFEHVDDVRGVGMVQAFTLVKNKAKRELFPDFGEIGTLCRDIFFRNNLIMRACGDHIVSAPPLVMTRAEVDEMLAVAERCLEEFEQTLKARGLA 459
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       


Chain B from PDB  Type:PROTEIN  Length:427
 aligned with Q7NWG4_CHRVO | Q7NWG4 from UniProtKB/TrEMBL  Length:459

    Alignment length:427
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       
         Q7NWG4_CHRVO    33 ARVMTRGEGVYLWDSEGNKIIDGMAGLWCVNVGYGRKDFAEAARRQMEELPFYNTFFKTTHPAVVELSSLLAEVTPAGFDRVFYTNSGSESVDTMIRMVRRYWDVQGKPEKKTLIGRWNGYHGSTIGGASLGGMKYMHEQGDLPIPGMAHIEQPWWYKHGKDMTPDEFGVVAARWLEEKILEIGADKVAAFVGEPIQGAGGVIVPPATYWPEIERICRKYDVLLVADEVICGFGRTGEWFGHQHFGFQPDLFTAAKGLSSGYLPIGAVFVGKRVAEGLIAGGDFNHGFTYSGHPVCAAVAHANVAALRDEGIVQRVKDDIGPYMQKRWRETFSRFEHVDDVRGVGMVQAFTLVKNKAKRELFPDFGEIGTLCRDIFFRNNLIMRACGDHIVSAPPLVMTRAEVDEMLAVAERCLEEFEQTLKARGLA 459
               SCOP domains d4ba5b_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh....ee..eehhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhhh.hhhhh.........eeee...hhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh.....eeeeehhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeeeeee....ee....hhhhhhhhhhhhhh.ee.eee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ba5 B  33 ARVMTRGEGVYLWDSEGNKIIDGMAGLWCVNVGYGRKDFAEAARRQMEELPFYNTFFKTTHPAVVELSSLLAEVTPAGFDRVFYTNSGSESVDTMIRMVRRYWDVQGKPEKKTLIGRWNGYHGSTIGGASLGGMKYMHEQGDLPIPGMAHIEQPWWYKHGKDMTPDEFGVVAARWLEEKILEIGADKVAAFVGEPIQGAGGVIVPPATYWPEIERICRKYDVLLVADEVICGFGRTGEWFGHQHFGFQPDLFTAAKGLSSGYLPIGAVFVGKRVAEGLIAGGDFNHGFTYSGHPVCAAVAHANVAALRDEGIVQRVKDDIGPYMQKRWRETFSRFEHVDDVRGVGMVQAFTLVKNKAKRELFPDFGEIGTLCRDIFFRNNLIMRACGDHIVSAPPLVMTRAEVDEMLAVAERCLEEFEQTLKARGLA 459
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4BA5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4BA5)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q7NWG4_CHRVO | Q7NWG4)
molecular function
    GO:0004015    adenosylmethionine-8-amino-7-oxononanoate transaminase activity    Catalysis of the reaction: 8-amino-7-oxononanoate + S-adenosyl-L-methionine(1+) = 7,8-diaminononanoate + S-adenosyl-4-methylthio-2-oxobutanoate.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0030170    pyridoxal phosphate binding    Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
    GO:0008483    transaminase activity    Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

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 Related Entries

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

UniProtKB/TrEMBL
        Q7NWG4_CHRVO | Q7NWG4: 4a6r 4a6t 4a6u 4a72 4ah3 4ba4

(-) Related Entries Specified in the PDB File

4a6r CRYSTAL STRUCTURE OF THE OMEGA TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM IN THE APO FORM, CRYSTALLISED FROM POLYACRYLIC ACID
4a6t CRYSTAL STRUCTURE OF THE OMEGA TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM IN COMPLEX WITH PLP
4a6u CRYSTAL STRUCTURE OF THE OMEGA TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM IN THE APO FORM, CRYSTALLISED FROM PEG 3350
4a72 CRYSTAL STRUCTURE OF THE OMEGA TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM IN A MIXTURE OF APO AND PLP -BOUND STATES
4ah3 CRYSTAL STRUCTURE OF THE HOLO OMEGA-TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM
4ba4 CRYSTAL STRUCTURE OF THE APO OMEGA-TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM