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(-) Description

Title :  CRYSTAL STRUCTURE OF T330S MUTANT OF RV3290C FROM M. TUBERCULOSIS
 
Authors :  S. M. Tripathi, R. Ramachandran
Date :  03 Apr 08  (Deposition) - 30 Jun 09  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Aminotransferase, Pyridoxal Phosphate, Plp, Rv3290C, Transferase, T330S Mutant, Lysine Amino Transferase, Mycobacterium Tuberculosis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. M. Tripathi, A. Agarwal, R. Ramachandran
Mutational Analysis Of Mycobacterium Tuberculosis Lysine Epsilon-Aminotransferase And Inhibitor Co-Crystal Structures, Reveals Distinct Binding Modes.
Biochem. Biophys. Res. Commun. V. 463 154 2015
PubMed-ID: 26003725  |  Reference-DOI: 10.1016/J.BBRC.2015.05.055

(-) Compounds

Molecule 1 - L-LYSINE EPSILON AMINOTRANSFERASE
    Chains: A
    EC Number: 2.6.1.36
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET
    Mutation: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: LYSINE EPSILON AMINOTRANSFERASE, L-LYSINE AMINOTRANSFERASE, LYSINE 6-AMINOTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:128 , ALA A:129 , PHE A:167 , HIS A:168 , GLU A:238 , ASP A:271 , VAL A:273 , GLN A:274 , LYS A:300 , SER A:330 , HOH A:2182 , HOH A:2183 , HOH A:2184 , HOH A:2185 , HOH A:2186BINDING SITE FOR RESIDUE PLP A1450

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_3PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.LAT_MYCTU268-305  1A:268-305
LAT_MYCTO268-305  1A:268-305
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AA_TRANSFER_CLASS_3PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.LAT_MYCTU268-305  2A:268-305
LAT_MYCTO268-305  2A:268-305

(-) Exons   (0, 0)

(no "Exon" information available for 2JJE)

(-) 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:435
 aligned with LAT_MYCTO | P9WQ76 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:435
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
            LAT_MYCTO    15 TTPDRVHEVLGRSMLVDGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT 449
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------Aminotran_3-2jjeA01 A:38-395                                                                                                                                                                                                                                                                                                                                          ------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh...................eee......eeee.hhhhhh......hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh........eeeee.........hhhhh...hhhhhh........ee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhh..eeeee............hhhhhh.....eeeehhhhh.eeeee.hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..eeeee..hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:268-305   ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jje A  15 TTPDRVHEVLGRSMLVDGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSSWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT 449
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     


Chain A from PDB  Type:PROTEIN  Length:435
 aligned with LAT_MYCTU | P9WQ77 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:435
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444     
            LAT_MYCTU    15 TTPDRVHEVLGRSMLVDGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSTWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT 449
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------Aminotran_3-2jjeA01 A:38-395                                                                                                                                                                                                                                                                                                                                          ------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh...................eee......eeee.hhhhhh......hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhhhhhh........eeeee.........hhhhh...hhhhhh........ee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhh..eeeee............hhhhhh.....eeeehhhhh.eeeee.hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..eeeee..hhhhhhhhhhhhhhh.ee.eee...eeee......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA_TRANSFER_CLASS_3  PDB: A:268-305   ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jje A  15 TTPDRVHEVLGRSMLVDGLDIVLDLTRSGGSYLVDAITGRRYLDMFTFVASSALGMNPPALVDDREFHAELMQAALNKPSNSDVYSVAMARFVETFARVLGDPALPHLFFVEGGALAVENALKAAFDWKSRHNQAHGIDPALGTQVLHLRGAFHGRSGYTLSLTNTKPTITARFPKFDWPRIDAPYMRPGLDEPAMAALEAEALRQARAAFETRPHDIACFVAEPIQGEGGDRHFRPEFFAAMRELCDEFDALLIFDEVQTGCGLTGTAWAYQQLDVAPDIVAFGKKTQVCGVMAGRRVDEVADNVFAVPSRLNSSWGGNLTDMVRARRILEVIEAEGLFERAVQHGKYLRARLDELAADFPAVVLDPRGRGLMCAFSLPTTADRDELIRQLWQRAVIVLPAGADTVRFRPPLTVSTAEIDAAIAAVRSALPVVT 449
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444
   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  (0, 0)

(no "SCOP Domain" information available for 2JJE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2JJE)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: PLP_aminotran (240)

(-) Gene Ontology  (9, 15)

Asymmetric Unit(hide GO term definitions)
Chain A   (LAT_MYCTO | P9WQ76)
molecular function
    GO:0045484    L-lysine 6-transaminase activity    Catalysis of the reaction: 2-oxoglutarate + L-lysine = L-glutamate + allysine.
    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: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.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.

Chain A   (LAT_MYCTU | P9WQ77)
molecular function
    GO:0003867    4-aminobutyrate transaminase activity    Catalysis of the reaction: 4-aminobutanoate + amino group acceptor = succinate semialdehyde + amino acid.
    GO:0045484    L-lysine 6-transaminase activity    Catalysis of the reaction: 2-oxoglutarate + L-lysine = L-glutamate + allysine.
    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.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0009450    gamma-aminobutyric acid catabolic process    The chemical reactions and pathways resulting in the breakdown of gamma-aminobutyric acid (GABA, 4-aminobutyrate), an amino acid which acts as a neurotransmitter in some organisms.

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  2.6.1.36
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 Related Entries

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

UniProtKB/Swiss-Prot
        LAT_MYCTO | P9WQ76: 2cin 2cjd 2cjg 2cjh 2jjf 2jjg 2jjh
        LAT_MYCTU | P9WQ77: 2cin 2cjd 2cjg 2cjh 2jjf 2jjg 2jjh

(-) Related Entries Specified in the PDB File

2jjf N328A MUTANT OF M. TUBERCULOSIS RV3290C
2jjg CRYSTAL STRUCTURE OF THE M. TUBERCULOSIS LYSINE-EPSILON AMINOTRANSFERASE (RV3290C) COMPLEXED TO AN INHIBITOR
2jjh E243 MUTANT OF M. TUBERCULOSIS RV3290C