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(-) Description

Title :  CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BIOA) FROM MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH A FRAGMENT HIT
 
Authors :  B. C. Finzel, D. Dai, T. W. Geders
Date :  17 Nov 14  (Deposition) - 15 Jul 15  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Inhibitor Complex Transaminase Plp, Transferase-Transferase Inhibitor Complex (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, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
13VQ2Ligand/Ion5-(PYRIDIN-2-YL)THIOPHENE-2-CARBOXAMIDE
2PLP4Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
13VQ1Ligand/Ion5-(PYRIDIN-2-YL)THIOPHENE-2-CARBOXAMIDE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
13VQ1Ligand/Ion5-(PYRIDIN-2-YL)THIOPHENE-2-CARBOXAMIDE
2PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:123 , GLY A:124 , SER A:125 , TYR A:157 , HIS A:158 , GLU A:220 , ASP A:254 , ILE A:256 , ALA A:257 , HOH A:608 , PRO B:317 , THR B:318binding site for residue PLP A 501
2AC2SOFTWAREPRO A:24 , TRP A:64 , PHE A:402 , MET B:91 , PHE B:92 , GLY B:93 , GLY B:316 , PRO B:317 , THR B:318binding site for residue 3VQ B 501
3AC3SOFTWAREPRO A:317 , THR A:318 , SER B:123 , 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:257binding site for residue PLP B 502
4AC4SOFTWARESER C:123 , GLY C:124 , SER C:125 , TYR C:157 , HIS C:158 , GLU C:220 , ASP C:254 , ILE C:256 , ALA C:257 , THR D:318binding site for residue PLP C 501
5AC5SOFTWARETYR C:25 , TRP C:64 , MET D:91 , PHE D:92 , GLY D:93 , GLY D:316 , PRO D:317 , THR D:318binding site for residue 3VQ D 501
6AC6SOFTWAREPRO C:317 , THR C:318 , GLY D:124 , SER D:125 , TYR D:157 , HIS D:158 , GLU D:220 , ASP D:254 , ILE D:256 , ALA D:257binding site for residue PLP D 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Glu A:31 -Ala A:32
2Val A:39 -Ala A:40
3Asp A:59 -Ala A:60
4Ala A:60 -Met A:61
5Gly C:308 -Ala C:309
6Ala C:309 -Ala C:310

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WYA)

(-) Sequences/Alignments

Asymmetric 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:420
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh..............eee......eeeee....eeeee..............hhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhhhhhhhhh.......eeee........hhhhhh..............ee........hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee.............hhhhhh....eeee...........eeeeeehhhhhhhh.............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeee....hhhhhhhhhhh..........eeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wya A   7 GLTPEQIIAVDGAHLWHPYSSIGREAVSPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGGTDVLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLV 433
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166      |181       191       201       211       221       231       241       251       261       271       281       291       301      |313       323       333       343       353       363       373       383       393       403       413       423       433
                                                                                                                                                                                                173|                                                                                                                              308|                                                                                                                          
                                                                                                                                                                                                 179                                                                                                                               311                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:422
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh............eeeeeee..eeeeee..eeeeeee.hhhhhh......hhhhhhhhhhhhhhh.......eeehhhhhhhhhhhhhh.......eee.hhhhhhhhhhhhhhhhhhhh......eeeee..........hhhhh...............ee.......hhhhhhhhhhhhhhhh..eeeeee...ee.....ee..hhhhhhhhhhhhhhh.eeeee............hhhhhh.....eeeehhhhhh.....eeeeehhhhhhhhh...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhhh.ee......eeee........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wya B   7 GLTPEQIIAVDGAHLWHPYSSIGRESPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGHSLWDVLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGAAGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLV 433
                                    16        26    ||  38        48        58        68        78        88        98       108       118       128       138       148       158       168   ||  181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431  
                                                   31|                                                                                                                                       172|  ||                                                                                                                                                                                                                                                             
                                                    34                                                                                                                                        175  ||                                                                                                                                                                                                                                                             
                                                                                                                                                                                                 178|                                                                                                                                                                                                                                                             
                                                                                                                                                                                                  180                                                                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:419
                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...........eeeeeee..eeeeee..eeeeeee.hhhhhh......hhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhhhh......eeeee.......hhhhhh.............eee.......hhhhhhhhhhhhhhh...eeeeee..............hhhhhhhhhhhhhh..eeeee............hhhhhh.....eeee...........eeeeehhhhhhhhhhh.............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wya C   7 GLTPEQIIAVDGAHLWHPYSSIGRSPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGTDVLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGAAGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLVG 434
                                    16        26   ||   39        49        59        69        79        89        99       109       119       129       139       149       159       169  ||   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425         
                                                  30|                                                                                                                                       172|                                                                                                                                                                                                                                                               
                                                   34                                                                                                                                        179                                                                                                                                                                                                                                                               


Chain D from PDB  Type:PROTEIN  Length:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               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..........eee.......hhhhhhhhhhhhhhhhh.eeeeee...ee.....ee..hhhhhhhhhhhhhh..eeeeee...........hhhhhh.....eeee...........eeeeeehhhhhhhh...............hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeee....hhhhhhhhhhhh.ee......eeee......hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4wya D   7 GLTPEQIIAVDGAHLWHPYSSIGSPVVAVAAHGAWLTLIRDGQPIEVLDAMSSWWTAIHGHGHPALDQALTTQLRVMNHVMFGGLTHEPAARLAKLLVDITPAGLDTVFFSDSGSVSVEVAAKMALQYWRGRGLPGKRRLMTWRGGYHGDTFLAMSICDPHGLAAQVFAPQVPRDYDPAYSAAFEAQLAQHAGELAAVVVEPVVQGAGGMRFHDPRYLHDLRDICRRYEVLLIFDEIATGFGRTGALFAADHAGVSPDIMCVGKALTGGYLSLAATLCTADVAHTISAGAAGALMHGPTFMANPLACAVSVASVELLLGQDWRTRITELAAGLTAGLDTARALPAVTDVRVCGAIGVIECDRPVDLAVATPAALDRGVWLRPFRNLVYAMPPYICTPAEITQITSAMVEVARLV 433
                                    16        26  ||    40        50        60        70        80        90       100       110       120       130       140       150       160       170 ||    189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429    
                                                 29|                                                                                                                                       172|                                                                                                                                                                                                                                                           
                                                  34                                                                                                                                        182
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  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 4WYA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

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  4wya
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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 4wyc 4wyd 4wye 4wyf 4wyg 4xew 4xjl 4xjm 4xjo 4xjp

(-) Related Entries Specified in the PDB File

4wyc 4wyd 4wye 4wyf 4wyg