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(-) Description

Title :  CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BIOA) FROM MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH A THIAZOLE INHIBITOR
 
Authors :  B. C. Finzel, R. Dai
Date :  13 Aug 14  (Deposition) - 04 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Inhibitor Complex Transaminase Plp, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Park, D. E. Casalena, D. J. Wilson, R. Dai, P. P. Nag, F. Liu, J. P. Boyce, J. A. Bittker, S. L. Schreiber, B. C. Finzel, D. Schnappinger, C. C. Aldrich
Target-Based Identification Of Whole-Cell Active Inhibitors Of Biotin Biosynthesis In Mycobacterium Tuberculosis.
Chem. Biol. V. 22 76 2015
PubMed-ID: 25556942  |  Reference-DOI: 10.1016/J.CHEMBIOL.2014.11.012

(-) 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, MT1619
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83331
    Strain: CDC 1551 / OSHKOSH
    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  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
13GS2Ligand/IonDIMETHYL (2R)-5-(3-FLUOROPHENYL)-1H-PYRROLO[1,2-C][1,3]THIAZOLE-6,7-DICARBOXYLATE 2-OXIDE
2CL1Ligand/IonCHLORIDE ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
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 , 3GS A:502 , HOH A:643 , HOH A:648 , HOH A:650 , HOH A:686 , HOH A:698 , PRO B:317 , THR B:318binding site for residue PLP A 501
2AC2SOFTWAREPRO A:24 , TYR A:25 , TRP A:64 , TYR A:157 , ARG A:400 , PHE A:402 , PLP A:501 , HOH A:686 , MET B:91 , GLY B:93 , GLY B:316 , PRO B:317 , THR B:318binding site for residue 3GS A 502
3AC3SOFTWAREHIS A:232 , PRO A:234 , HIS A:271 , HOH A:733binding site for residue PEG A 503
4AC4SOFTWARETHR A:318 , HOH A:644 , 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 , 3GS B:502 , HOH B:659 , HOH B:662 , HOH B:666 , HOH B:674binding 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 , TYR B:157 , ARG B:400 , PLP B:501 , HOH B:662binding site for residue 3GS B 502
6AC6SOFTWARETHR B:152 , TRP B:153 , GLY B:156 , HIS B:158 , ILE B:167 , VAL B:219 , GLU B:220 , GLN B:224binding site for residue EDO B 503
7AC7SOFTWAREVAL B:222binding site for residue EDO B 505
8AC8SOFTWARELEU B:337 , GLN B:339 , ASP B:340binding site for residue EDO B 506
9AC9SOFTWAREHIS A:271 , ARG B:246 , TYR B:247 , HOH B:601binding site for residue EDO B 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W1V)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:176 -Leu A:177

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W1V)

(-) Exons   (0, 0)

(no "Exon" information available for 4W1V)

(-) 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:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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..................eee.......hhhhhhhhhhhhhhhhh.eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeee...........eeeeeehhhhhhhhh..............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w1v A   8 LTPEQIIAVDGAHLWHPYSSIGRSPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGGMHSLWTDVLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGAAGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLVGS 435
                                    17        27  ||    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430     
                                                 30|                                                                                                                                                                                                                                                                                                                                                                                                                 
                                                  34                                                                                                                                                                                                                                                                                                                                                                                                                 


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......hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhh.......eeeee.......hhhhhhh......hhhhhh......eee.......hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeee...........eeeeehhhhhhhhhhh.............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhh..ee......eeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w1v B   7 GLTPEQIIAVDGAHLWHPYSSIGREAVSPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGGMHSLWTDVLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGAAGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLVGS 435
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426
   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 4W1V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W1V)

(-) Gene Ontology  (8, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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    Ser A:176 - Leu A:177   [ RasMol ]  
 

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  4w1v
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  BIOA_MYCTO | P9WQ80
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  BIOA_MYCTU | P9WQ81
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  2.6.1.62
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 Related Entries

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

UniProtKB/Swiss-Prot
        BIOA_MYCTO | P9WQ80: 3bv0 3lv2 3tft 3tfu 4cxq 4cxr 4mqp 4mqq 4mqr 4w1w 4w1x
        BIOA_MYCTU | P9WQ81: 3bv0 3lv2 3tft 3tfu 4cxq 4cxr 4mqp 4mqq 4mqr 4w1w 4w1x 4wya 4wyc 4wyd 4wye 4wyf 4wyg 4xew 4xjl 4xjm 4xjo 4xjp

(-) Related Entries Specified in the PDB File

4w1w 4w1x