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(-) Description

Title :  CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BIOA) FROM MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH 7-(DIETHYLAMINO)-3-(THIOPHENE-2-CARBONYL)-2H-CHROMEN-2-ONE
 
Authors :  B. C. Finzel, D. Ran
Date :  13 Aug 14  (Deposition) - 04 Feb 15  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
13G82Ligand/Ion7-(DIETHYLAMINO)-3-(THIOPHEN-2-YLCARBONYL)-2H-CHROMEN-2-ONE
2CL1Ligand/IonCHLORIDE ION
3EDO8Ligand/Ion1,2-ETHANEDIOL
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
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:708 , HOH A:759 , HOH A:785 , HOH A:788 , HOH A:838 , PRO B:317 , THR B:318 , HOH B:695binding site for residue PLP A 501
02AC2SOFTWAREPRO A:24 , TYR A:25 , TRP A:64 , GLY A:172 , ARG A:400 , HOH A:793 , HOH A:852 , HOH A:922 , GLY B:93 , GLY B:316 , PRO B:317 , THR B:318binding site for residue 3G8 A 502
03AC3SOFTWAREHIS A:271 , ALA A:272 , HOH A:602 , HOH A:616 , ARG B:246binding site for residue EDO A 503
04AC4SOFTWAREPRO A:234 , HIS A:271 , HOH A:616 , HOH A:796 , HOH A:933binding site for residue EDO A 504
05AC5SOFTWAREARG A:154 , PHE A:187 , ALA A:188 , PRO A:189 , HOH A:822 , HOH A:897 , HOH A:903binding site for residue EDO A 505
06AC6SOFTWARESER A:200 , ALA A:201 , GLU A:204 , ASP A:239 , ASP A:242 , ILE A:243 , ARG A:246binding site for residue EDO A 506
07AC7SOFTWAREARG A:344 , ILE A:413 , CYS A:414 , THR A:415 , PRO A:416 , HOH A:782 , HOH A:987binding site for residue EDO A 507
08AC8SOFTWAREPRO A:317 , THR A:318 , HOH A:696 , 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:681 , HOH B:709 , HOH B:741 , HOH B:742binding site for residue PLP B 501
09AC9SOFTWAREGLY A:93 , GLY A:316 , PRO A:317 , THR A:318 , PRO B:24 , TYR B:25 , TRP B:64 , GLY B:172 , HOH B:817binding site for residue 3G8 B 502
10AD1SOFTWARESER B:275binding site for residue CL B 503
11AD2SOFTWAREVAL B:222 , HIS B:232 , PRO B:234binding site for residue EDO B 504
12AD3SOFTWAREVAL B:108 , ASP B:109 , THR B:111 , PRO B:112 , ALA B:113 , GLY B:114 , LEU B:115 , HOH B:717 , HOH B:804 , HOH B:848binding site for residue EDO B 505
13AD4SOFTWARETRP B:45 , GLU B:56binding site for residue EDO B 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4W1W)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Thr A:179 -Asp A:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4W1W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4W1W)

(-) Exons   (0, 0)

(no "Exon" information available for 4W1W)

(-) 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......hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhhh......hhhhh.......eee.......hhhhhhhhhhhhhhhhh.eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeee...........eeeeeehhhhhhhhhh.............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w1w 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:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..............eeeeeee..eeeeee..eeeeeee.hhhhhh......hhhhhhhhhhhhh.........eehhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhh.......hhhhh.......eee.......hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeee...........eeeeehhhhhhhhhhh.............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4w1w B   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
   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 4W1W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4W1W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4W1W)

(-) Gene Ontology  (8, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  4w1w
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  BIOA_MYCTO | P9WQ80
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  BIOA_MYCTU | P9WQ81
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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 4w1v 4w1x
        BIOA_MYCTU | P9WQ81: 3bv0 3lv2 3tft 3tfu 4cxq 4cxr 4mqp 4mqq 4mqr 4w1v 4w1x 4wya 4wyc 4wyd 4wye 4wyf 4wyg 4xew 4xjl 4xjm 4xjo 4xjp

(-) Related Entries Specified in the PDB File

4w1w 4w1x