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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 :  1.60
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
    Chains: A, B
    EC Number: 2.6.1.62
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BIOA, RV1568, MTCY336.35C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
    Synonym: 7,8-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  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
141N2Ligand/Ion1-{4-[4-(1,3-BENZODIOXOL-5-YLCARBONYL)PIPERAZIN-1-YL]PHENYL}ETHANONE
2EDO5Ligand/Ion1,2-ETHANEDIOL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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:733 , HOH A:755 , HOH A:764 , HOH A:774 , HOH A:872 , PRO B:317 , THR B:318 , HOH B:688binding site for residue PLP A 501
02AC2SOFTWARETYR A:25 , TRP A:64 , GLY A:156 , TYR A:157 , CYS A:168 , GLY A:172 , GLY A:173 , ALA A:226 , GLY A:227 , ARG A:400 , PHE A:402 , HOH A:779 , HOH A:798 , MET B:91 , PHE B:92 , GLY B:93 , GLY B:316 , PRO B:317 , THR B:318binding site for residue 41N A 502
03AC3SOFTWARELEU A:385 , PHE A:402 , ARG A:403 , HOH A:815 , HOH A:893 , HOH A:1022binding site for residue EDO A 503
04AC4SOFTWAREARG A:193 , VAL A:222 , HIS A:232 , ASP A:233 , PRO A:234 , HOH A:1066 , HOH A:1067binding site for residue PEG A 504
05AC5SOFTWAREMET A:91 , PHE A:92 , GLY A:93 , GLY A:316 , PRO A:317 , THR A:318 , TYR B:25 , TRP B:64 , GLY B:156 , TYR B:157 , CYS B:168 , GLY B:172 , GLY B:173 , ALA B:226 , GLY B:227 , ARG B:400 , PHE B:402 , HOH B:773 , HOH B:920binding site for residue 41N B 502
06AC6SOFTWAREGLU B:56 , HOH B:610binding site for residue EDO B 503
07AC7SOFTWAREASP A:122 , PHE A:319 , HOH A:737 , ASP B:122 , SER B:123 , GLY B:282 , SER B:291 , LEU B:292 , HOH B:798binding site for residue EDO B 504
08AC8SOFTWAREGLY B:355 , THR B:358 , THR B:420 , THR B:423 , SER B:424binding site for residue EDO B 505
09AC9SOFTWAREARG B:193 , HIS B:232 , ASP B:233 , PRO B:234 , HIS B:271binding site for residue PEG B 506
10AD1SOFTWAREHIS A:271 , ALA A:272 , ARG B:246 , TYR B:247binding site for residue EDO B 507
11AD2SOFTWAREPRO A:317 , THR A:318 , HOH A:737 , TRP B:64 , TRP B:65 , THR B:66 , GLY B:124 , SER B:125 , TYR B:157 , HIS B:158 , GLY B:159 , GLU B:220 , ASP B:254 , ILE B:256 , ALA B:257 , GLY B:282 , ALA B:284 , LEU B:285 , HOH B:710 , HOH B:720 , HOH B:725 , HOH B:749 , HOH B:798binding site for Di-peptide PLP B 501 and LYS B 283

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XJP)

(-) 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:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............eeeeeee..eeeeee..eeeeeee.hhhhhh......hhhhhhhhhhhhh.........eehhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhh......hhhhhh......eee.......hhhhhhhhhhhhhhhh..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
                 4xjp A   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         


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......hhhhhh......eee.......hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeee...........eeeeeehhhhhhhhhh.............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhh..ee......eeee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xjp 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)
  - → 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 4XJP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 | P9WQ81: 3bv0 3lv2 3tft 3tfu 4cxq 4cxr 4mqp 4mqq 4mqr 4w1v 4w1w 4w1x 4wya 4wyc 4wyd 4wye 4wyf 4wyg 4xew 4xjl 4xjm 4xjo

(-) Related Entries Specified in the PDB File

4xjl 4xjm 4xjo