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(-) Description

Title :  CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BIOA) FROM MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH AN INHIBITOR OPTIMIZED FROM HTS LEAD
 
Authors :  B. C. Finzel, R. Dai
Date :  08 Jan 15  (Deposition) - 20 Jan 16  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor Complex Transaminase Plp, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Liu, S. Dawadi, K. M. Maize, R. Dai, S. W. Park, D. Schnappinger, B. C. Finzel, C. C. Aldrich
Structure-Based Optimization Of Pyridoxal 5'-Phosphate-Dependent Transaminase Enzyme (Bioa) Inhibitor That Target Biotin Biosynthesis In Mycobacterium Tuberculosis.
J. Med. Chem. 2017
PubMed-ID: 28594172  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00189
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
    ChainsA, B
    EC Number2.6.1.62
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneBIOA, RV1568, MTCY336.35C
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid83332
    StrainATCC 25618 / H37RV
    Synonym7,8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE,DAPA AMINOTRANSFERASE,8-DIAMINONONANOATE SYNTHASE,DANS,DIAMINOPELARGONIC ACID SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
141O2Ligand/Ion5-[4-(3-CHLOROBENZOYL)PIPERAZIN-1-YL]-1H-INDEN-1-ONE
2CL1Ligand/IonCHLORIDE ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
5SO41Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:124 , SER A:125 , TYR A:157 , HIS A:158 , GLY A:159 , GLU A:220 , ASP A:254 , ILE A:256 , ALA A:257 , LYS A:283 , HOH A:708 , HOH A:728 , HOH A:745 , HOH A:762 , PRO B:317 , THR B:318 , HOH B:815 , HOH B:816binding site for residue PLP A 501
2AC2SOFTWARETYR A:25 , TRP A:64 , GLY A:156 , TYR A:157 , GLY A:172 , GLY A:173 , ALA A:226 , ARG A:400 , ARG A:403 , HOH A:790 , MET B:91 , PHE B:92 , GLY B:93 , GLY B:316 , PRO B:317 , THR B:318binding site for residue 41O A 502
3AC3SOFTWAREARG A:344 , ILE A:413 , CYS A:414 , THR A:415 , PRO A:416binding site for residue EDO A 503
4AC4SOFTWAREPRO A:317 , THR A:318 , HOH A:922 , GLY B:124 , SER B:125 , TYR B:157 , HIS B:158 , GLU B:220 , ASP B:254 , ILE B:256 , ALA B:257 , LYS B:283 , HOH B:709 , HOH B:712 , HOH B:764 , HOH B:777 , HOH B:818binding site for residue PLP B 501
5AC5SOFTWAREMET A:91 , PHE A:92 , GLY A:93 , GLY A:316 , PRO A:317 , THR A:318 , PRO B:24 , TYR B:25 , TRP B:64 , GLY B:156 , TYR B:157 , GLY B:172 , GLY B:173 , ALA B:226binding site for residue 41O B 502
6AC6SOFTWARETRP B:139 , CYS B:244 , GLU B:248 , VAL B:249 , LEU B:250 , HOH B:829binding site for residue SO4 B 503
7AC7SOFTWAREGLY A:355 , THR A:423 , SER A:424 , HOH A:671 , HOH A:676binding site for residue CL B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XJO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XJO)

(-) 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:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............eeeeeee..eeeeee..eeeeeee.hhhhhh......hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhh......hhhhhh......eee.......hhhhhhhhhhhhhhhhh.eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeee...........eeeeeehhhhhhhhhh.............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhh..ee......eeee......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xjo A   8 LTPEQIIAVDGAHLWHPYSSIGREAVSPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGGMHSLWTDVLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGAAGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLVGS 435
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427        

Chain B from PDB  Type:PROTEIN  Length:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............eeeeeee..eeeeee..eeeeeee.hhhhhh......hhhhhhhhhhhhh.........eehhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhh.......eeeee.......hhhhhhh......hhhhh.......eee.......hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeee...........eeeeeehhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhh..ee......eeee......hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xjo B   8 LTPEQIIAVDGAHLWHPYSSIGREAVSPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGGMHSLWTDVLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGAAGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLVGSL 436
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427         

   Legend:   → Mismatch (orange background)
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    → 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 4XJO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BIOA_MYCTU | P9WQ813bv0 3lv2 3tft 3tfu 4cxq 4cxr 4mqp 4mqq 4mqr 4w1v 4w1w 4w1x 4wya 4wyc 4wyd 4wye 4wyf 4wyg 4xew 4xjl 4xjm 4xjp

(-) Related Entries Specified in the PDB File

4xjl 4xjm 4xjp