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(-) Description

Title :  CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BIOA) FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH A FRAGMENT HIT
 
Authors :  R. Dai, B. C. Finzel
Date :  17 Nov 14  (Deposition) - 08 Jul 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.62
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Complex, Transaminase, Plp, Fragment, Transferase/Transferase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Dai, T. W. Geders, F. Liu, S. W. Park, D. Schnappinger, C. C. Aldrich, B. C. Finzel
Fragment-Based Exploration Of Binding Site Flexibility In Mycobacterium Tuberculosis Bioa.
J. Med. Chem. V. 58 5208 2015
PubMed-ID: 26068403  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00092

(-) 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
    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, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
13W13Ligand/Ion1-{4-[(4-CHLORO-1H-PYRAZOL-1-YL)METHYL]PHENYL}METHANAMINE
2EDO11Ligand/Ion1,2-ETHANEDIOL
3EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:65 , GLY A:124 , SER A:125 , TYR A:157 , HIS A:158 , GLU A:220 , ASP A:254 , ILE A:256 , ALA A:257 , LYS A:283 , 3W1 A:503 , HOH A:706 , HOH A:721 , HOH A:736 , HOH A:745 , GLY B:316 , PRO B:317 , THR B:318binding site for residue PLP A 501
02AC2SOFTWARETYR A:25 , SER A:27 , GLU A:31 , TRP A:64 , ARG A:400 , 3W1 A:503 , HOH A:740 , HOH A:807 , GLY B:93 , GLY B:94binding site for residue EPE A 502
03AC3SOFTWARETYR A:25 , TRP A:64 , TRP A:65 , TYR A:157 , ALA A:226 , ARG A:400 , PHE A:402 , PLP A:501 , EPE A:502 , HOH A:703 , HOH A:737 , GLY B:316 , THR B:318binding site for residue 3W1 A 503
04AC4SOFTWAREVAL A:222 , HIS A:232 , HOH A:878 , HOH A:996binding site for residue EDO A 504
05AC5SOFTWAREARG A:193 , ARG A:230 , PHE A:231 , ARG A:369 , HOH A:608 , HOH A:805 , HOH A:906 , HOH A:1024binding site for residue EDO A 505
06AC6SOFTWAREARG A:344 , ILE A:413 , CYS A:414 , THR A:415 , PRO A:416 , HOH A:827 , HOH A:974binding site for residue EDO A 506
07AC7SOFTWAREALA A:113 , GLY A:273 , SER A:275 , HOH A:653 , HOH A:788binding site for residue EDO A 507
08AC8SOFTWAREGLY A:93 , GLY A:94 , PRO B:24 , TYR B:25 , SER B:27 , GLU B:31 , TRP B:64 , LEU B:385 , ARG B:400 , 3W1 B:503 , HOH B:724 , HOH B:795binding site for residue EPE B 502
09AC9SOFTWAREGLY A:316 , THR A:318 , TYR B:25 , TRP B:64 , TRP B:65 , TYR B:157 , ALA B:226 , ARG B:400 , PHE B:402 , PLP B:501 , EPE B:502 , HOH B:672 , HOH B:712binding site for residue 3W1 B 503
10AD1SOFTWARETRP B:45 , GLU B:56binding site for residue EDO B 504
11AD2SOFTWAREALA A:211 , GLY A:212 , HOH A:616 , HOH A:624 , ARG B:154 , HIS B:171 , HOH B:611 , HOH B:630binding site for residue EDO B 505
12AD3SOFTWAREARG B:193 , VAL B:222 , PHE B:231 , HIS B:232 , ASP B:233 , PRO B:234 , HIS B:271 , HOH B:846 , HOH B:847 , HOH B:860 , HOH B:943binding site for residue 3W1 B 506
13AD4SOFTWAREHIS B:23 , GLU B:31 , VAL B:33 , SER B:34 , PRO B:35 , EDO B:508 , HOH B:710 , HOH B:802 , HOH B:962binding site for residue EDO B 507
14AD5SOFTWAREASP B:17 , GLY B:18 , LEU B:21 , HIS B:23 , ILE B:28 , PRO B:35 , EDO B:507 , HOH B:869 , HOH B:961binding site for residue EDO B 508
15AD6SOFTWARELEU A:144 , ARG B:154 , GLN B:185 , VAL B:186 , PHE B:187 , HOH B:601 , HOH B:605 , HOH B:649binding site for residue EDO B 509
16AD7SOFTWAREHIS A:271 , ALA A:272 , ARG B:246 , EDO B:511 , HOH B:606binding site for residue EDO B 510
17AD8SOFTWAREARG B:246 , TYR B:247 , EDO B:510 , HOH B:603binding site for residue EDO B 511
18AD9SOFTWAREGLY A:316 , PRO A:317 , THR A:318 , PHE A:319 , TRP B:64 , TRP B:65 , GLY B:124 , SER B:125 , TYR B:157 , HIS B:158 , GLU B:220 , ASP B:254 , ILE B:256 , ALA B:257 , GLY B:282 , ALA B:284 , LEU B:285 , THR B:286 , 3W1 B:503 , HOH B:698 , HOH B:702 , HOH B:716 , HOH B:758 , HOH B:762 , HOH B:861binding site for Di-peptide PLP B 501 and LYS B 283

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 2)

Asymmetric/Biological Unit
No.Residues
1Ala B:307 -Gly B:308

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WYG)

(-) 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.......hhhhhh........hhhhhhhh...eee.......hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeeehhhhhh.....eeeeeehhhhhhh................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhh..ee......eeee......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wyg 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.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhh........hhhhhhhh...eee.......hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeeehhhhhh.....eeeeeehhhhhhhh...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhh..ee......eeee......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wyg 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 4WYG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:307 - Gly B:308   [ RasMol ]  
 

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

(-) Related Entries Specified in the PDB File

4wya 4wyc 4wyd 4wye 4wyf