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(-) Description

Title :  CRYSTAL STRUCTURE OF THE OMEGA TRANSAMINASE FROM CHROMOBACTERIUM VIOLACEUM IN THE APO FORM, CRYSTALLISED FROM POLYACRYLIC ACID
 
Authors :  D. T. Logan, M. Hakansson, K. Yengo, M. Svedendahl Humble, K. Engelmark Cassimjee, B. Walse, V. Abedi, H. -J. Federsel, P. Bergl
Date :  08 Nov 11  (Deposition) - 25 Jan 12  (Release) - 01 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase, Plp-Binding Enzyme, Transaminase Fold Type I (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Svedendahl Humble, K. Engelmark Cassimjee, M. Hakansson, Y. R. Kimbung, B. Walse, V. Abedi, H. -J. Federsel, P. Berglund, D. T. Logan
Crystal Structures Of The Chromobacterium Violaceum Omega- Transaminase Reveal Major Structural Rearrangements Upon Binding Of Coenzyme Plp.
Febs J. V. 279 779 2012
PubMed-ID: 22268978  |  Reference-DOI: 10.1111/J.1742-4658.2011.08468.X

(-) Compounds

Molecule 1 - OMEGA TRANSAMINASE
    Chains: A, B
    EC Number: 2.6.1.18, 2.6.1.62
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A
    Expression System Vector Type: PLASMID
    Organism Scientific: CHROMOBACTERIUM VIOLACEUM
    Organism Taxid: 536
    Synonym: PROBABLE AMINOTRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1TA82Ligand/IonPOLYACRYLIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:119 , GLY A:120 , SER A:121 , TYR A:153 , SER A:156 , THR A:157 , HOH A:2140 , HOH A:2141 , HOH A:2438 , THR B:117 , ASN B:118 , GLU B:122 , THR B:126 , ARG B:129BINDING SITE FOR RESIDUE TA8 A1460
2AC2SOFTWARETHR A:117 , ASN A:118 , GLU A:122 , THR A:126 , ARG A:129 , HOH A:2123 , HOH A:2132 , SER B:119 , GLY B:120 , SER B:121 , TYR B:153 , SER B:156 , THR B:157 , HOH B:2100 , HOH B:2404BINDING SITE FOR RESIDUE TA8 B1460

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4A6R)

(-) 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 4A6R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4A6R)

(-) Exons   (0, 0)

(no "Exon" information available for 4A6R)

(-) 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:423
 aligned with Q7NWG4_CHRVO | Q7NWG4 from UniProtKB/TrEMBL  Length:459

    Alignment length:426
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453      
         Q7NWG4_CHRVO    34 RVMTRGEGVYLWDSEGNKIIDGMAGLWCVNVGYGRKDFAEAARRQMEELPFYNTFFKTTHPAVVELSSLLAEVTPAGFDRVFYTNSGSESVDTMIRMVRRYWDVQGKPEKKTLIGRWNGYHGSTIGGASLGGMKYMHEQGDLPIPGMAHIEQPWWYKHGKDMTPDEFGVVAARWLEEKILEIGADKVAAFVGEPIQGAGGVIVPPATYWPEIERICRKYDVLLVADEVICGFGRTGEWFGHQHFGFQPDLFTAAKGLSSGYLPIGAVFVGKRVAEGLIAGGDFNHGFTYSGHPVCAAVAHANVAALRDEGIVQRVKDDIGPYMQKRWRETFSRFEHVDDVRGVGMVQAFTLVKNKAKRELFPDFGEIGTLCRDIFFRNNLIMRACGDHIVSAPPLVMTRAEVDEMLAVAERCLEEFEQTLKARGLA 459
               SCOP domains d4a6ra_ 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......---......eeee...hhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh.....eeeeehhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeee.............hhhhhhhhhhhhhh.ee.eee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4a6r A  34 RVMTRGEGVYLWDSEGNKIIDGMAGLWCVNVGYGRKDFAEAARRQMEELPFYNTFFKTTHPAVVELSSLLAEVTPAGFDRVFYTNSGSESVDTMIRMVRRYWDVQGKPEKKTLIGRWNGYHGSTIGGASLGGMKYMH---DLPIPGMAHIEQPWWYKHGKDMTPDEFGVVAARWLEEKILEIGADKVAAFVGEPIQGAGGVIVPPATYWPEIERICRKYDVLLVADEVICGFGRTGEWFGHQHFGFQPDLFTAAKGLSSGYLPIGAVFVGKRVAEGLIAGGDFNHGFTYSGHPVCAAVAHANVAALRDEGIVQRVKDDIGPYMQKRWRETFSRFEHVDDVRGVGMVQAFTLVKNKAKRELFPDFGEIGTLCRDIFFRNNLIMRACGDHIVSAPPLVMTRAEVDEMLAVAERCLEEFEQTLKARGLA 459
                                    43        53        63        73        83        93       103       113       123       133       143       153       163      |  -|      183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453      
                                                                                                                                                                  170 174                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:422
 aligned with Q7NWG4_CHRVO | Q7NWG4 from UniProtKB/TrEMBL  Length:459

    Alignment length:426
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453      
         Q7NWG4_CHRVO    34 RVMTRGEGVYLWDSEGNKIIDGMAGLWCVNVGYGRKDFAEAARRQMEELPFYNTFFKTTHPAVVELSSLLAEVTPAGFDRVFYTNSGSESVDTMIRMVRRYWDVQGKPEKKTLIGRWNGYHGSTIGGASLGGMKYMHEQGDLPIPGMAHIEQPWWYKHGKDMTPDEFGVVAARWLEEKILEIGADKVAAFVGEPIQGAGGVIVPPATYWPEIERICRKYDVLLVADEVICGFGRTGEWFGHQHFGFQPDLFTAAKGLSSGYLPIGAVFVGKRVAEGLIAGGDFNHGFTYSGHPVCAAVAHANVAALRDEGIVQRVKDDIGPYMQKRWRETFSRFEHVDDVRGVGMVQAFTLVKNKAKRELFPDFGEIGTLCRDIFFRNNLIMRACGDHIVSAPPLVMTRAEVDEMLAVAERCLEEFEQTLKARGLA 459
               SCOP domains d4a6rb_ B: 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......----.....eeee...hhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh.....eeeeehhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee..eeeeee.............hhhhhhhhhhhhhh.ee.eee..eeee......hhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4a6r B  34 RVMTRGEGVYLWDSEGNKIIDGMAGLWCVNVGYGRKDFAEAARRQMEELPFYNTFFKTTHPAVVELSSLLAEVTPAGFDRVFYTNSGSESVDTMIRMVRRYWDVQGKPEKKTLIGRWNGYHGSTIGGASLGGMKYMH----LPIPGMAHIEQPWWYKHGKDMTPDEFGVVAARWLEEKILEIGADKVAAFVGEPIQGAGGVIVPPATYWPEIERICRKYDVLLVADEVICGFGRTGEWFGHQHFGFQPDLFTAAKGLSSGYLPIGAVFVGKRVAEGLIAGGDFNHGFTYSGHPVCAAVAHANVAALRDEGIVQRVKDDIGPYMQKRWRETFSRFEHVDDVRGVGMVQAFTLVKNKAKRELFPDFGEIGTLCRDIFFRNNLIMRACGDHIVSAPPLVMTRAEVDEMLAVAERCLEEFEQTLKARGLA 459
                                    43        53        63        73        83        93       103       113       123       133       143       153       163      |  - |     183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453      
                                                                                                                                                                  170  175
   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 4A6R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4A6R)

(-) 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: 4a6t 4a6u 4a72 4ah3 4ba4 4ba5

(-) Related Entries Specified in the PDB File

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