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(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS DPRE1 IN COMPLEX WITH PBTZ169
 
Authors :  J. Neres, F. Pojer, S. T. Cole
Date :  25 Oct 13  (Deposition) - 19 Feb 14  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.88
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Decaprenylphosphoryl-Beta-D-Ribose Oxidase, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Makarov, B. Lechartier, M. Zhang, J. Neres, A. M. Van Der Sar, S. A. Raadsen, R. C. Hartkoorn, O. B. Ryabova, A. Vocat, L. A. Decosterd N. Widmer, T. Buclin, W. Bitter, K. Andries, F. Pojer, P. J. Dyson, S. T. Cole
Towards A New Combination Therapy For Tuberculosis With Nex Generation Benzothiazinones.
Embo Mol Med V. 6 372 2014
PubMed-ID: 24500695  |  Reference-DOI: 10.1002/EMMM.201303575

(-) Compounds

Molecule 1 - DECAPRENYLPHOSPHORYL-BETA-D-RIBOSE OXIDASE
    Chains: A, B
    EC Number: 1.-.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: DPRE1, MT3898, RV3790
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: H37RV
    Synonym: DPRE1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
126J2Ligand/Ion2-(4-(CYCLOHEXYLMETHYL)PIPERAZIN-1-YL)-8-NITRO-6-(TRIFLUOROMETHYL)-4H-BENZO[E][1,3]THIAZIN-4-ONE, BOUNDFORM
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL4Ligand/IonGLYCEROL
4IMD1Ligand/IonIMIDAZOLE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
126J1Ligand/Ion2-(4-(CYCLOHEXYLMETHYL)PIPERAZIN-1-YL)-8-NITRO-6-(TRIFLUOROMETHYL)-4H-BENZO[E][1,3]THIAZIN-4-ONE, BOUNDFORM
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL3Ligand/IonGLYCEROL
4IMD-1Ligand/IonIMIDAZOLE
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
126J1Ligand/Ion2-(4-(CYCLOHEXYLMETHYL)PIPERAZIN-1-YL)-8-NITRO-6-(TRIFLUOROMETHYL)-4H-BENZO[E][1,3]THIAZIN-4-ONE, BOUNDFORM
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL1Ligand/IonGLYCEROL
4IMD1Ligand/IonIMIDAZOLE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:117 , GLY A:133 , LYS A:134 , SER A:228 , LYS A:367 , ASN A:385 , CYS A:387 , LYS A:418 , FAD A:502 , HOH A:690BINDING SITE FOR RESIDUE 26J A 501
2AC2SOFTWARETRP A:16 , ILE A:52 , ALA A:53 , ARG A:54 , GLY A:55 , LEU A:56 , GLY A:57 , ARG A:58 , SER A:59 , TYR A:60 , ASN A:63 , ALA A:64 , MET A:74 , ALA A:94 , PRO A:116 , GLY A:117 , THR A:118 , VAL A:121 , THR A:122 , GLY A:124 , GLY A:125 , ALA A:128 , CYS A:129 , ILE A:131 , HIS A:132 , ASN A:178 , GLY A:179 , GLY A:182 , ILE A:184 , TYR A:415 , ALA A:417 , 26J A:501 , HOH A:629 , HOH A:633 , HOH A:692BINDING SITE FOR RESIDUE FAD A 502
3AC3SOFTWARETRP A:230 , PHE A:231 , TYR A:297BINDING SITE FOR RESIDUE GOL A 503
4AC4SOFTWARESER A:82 , ASP A:84 , THR A:87 , LEU A:89 , THR A:188 , IMD B:504BINDING SITE FOR RESIDUE GOL A 504
5AC5SOFTWAREASP B:204 , ASP B:218 , ARG B:223 , ARG B:247 , HOH B:630BINDING SITE FOR RESIDUE GOL A 505
6AC6SOFTWAREGLY B:117 , HIS B:132 , GLY B:133 , LYS B:134 , VAL B:365 , LYS B:367 , ASN B:385 , CYS B:387 , LYS B:418 , FAD B:502 , HOH B:657BINDING SITE FOR RESIDUE 26J B 501
7AC7SOFTWARETRP B:16 , ILE B:52 , ALA B:53 , ARG B:54 , GLY B:55 , LEU B:56 , GLY B:57 , ARG B:58 , SER B:59 , TYR B:60 , ASN B:63 , ALA B:64 , ALA B:94 , PRO B:116 , GLY B:117 , THR B:118 , VAL B:121 , THR B:122 , GLY B:124 , GLY B:125 , ALA B:128 , CYS B:129 , ILE B:131 , HIS B:132 , ASN B:178 , GLY B:179 , GLY B:182 , ILE B:184 , TYR B:415 , ALA B:417 , 26J B:501 , HOH B:610 , HOH B:645BINDING SITE FOR RESIDUE FAD B 502
8AC8SOFTWAREPRO A:107 , PHE A:108 , ASN B:78 , THR B:79 , ILE B:80 , GLN B:100BINDING SITE FOR RESIDUE GOL B 503
9AC9SOFTWARESER A:82 , ASP A:84 , GOL A:504 , SER B:82 , ASP B:84BINDING SITE FOR RESIDUE IMD B 504

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Gly A:46 -Gly A:47
2Pro A:237 -Pro A:238
3Pro A:270 -Gln A:271
4Gly B:46 -Gly B:47
5Pro B:237 -Pro B:238

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4NCR)

(-) 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:428
                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........eeeeeee..hhhhhhhhhhhhhhh.....eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhhh....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee....eeeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhh...........hhhhhhhhhhhhhhhhh.eeeeeee......eeeeeeeee..hhhhhhhhhhhhhhh.......eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee.hhhh...hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ncr A   6 ATTTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPQANKYTFGPIGELWYRKSGTYRGKVQNLTQFYGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 461
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265     ||287       297       307      |333       343       353       363       373       383       393       403       413       423       433       443       453        
                                                                                                                                                                                                                                                                                                   271|                           314|                                                                                                                                  
                                                                                                                                                                                                                                                                                                    284                            331                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:413
                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee........eeeeeee..hhhhhhhhhhhhhhh.....eeee...............eeee......eeeee....eeeee...hhhhhhhhhh...ee..........hhhhhhhh.....hhhhhhhhhh.eeeeeee.....eeee.....hhhhhhhhh.......eeeeeeee.ee....eeeeeeee..hhhhhhhhhhhhhhhhh.eeeeee...........eeeeeeee.hhhhhhhhhh..........hhhhh.eeeeeee.hhhh.eeeeeeeee..hhhhhhhhhhhhhhh.......eeeee.............eeeeeeeee...hhhhhhhhhhhhhhhh..ee.hhhh...hhhhhhhhh.hhhhhhhhhhhhh......hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ncr B   8 TTATRLTGWGRTAPSVANVLRTPDAEMIVKAVARVAESGGGRGAIARGLGRSYGDNAQNGGGLVIDMTPLNTIHSIDADTKLVDIDAGVNLDQLMKAALPFGLWVPVLPGTRQVTVGGAIACDIHGKNHHSAGSFGNHVRSMDLLTADGEIRHLTPTGEDAELFWATVGGNGLTGIIMRATIEMTPTSTAYFIADGDVTASLDETIALHSDGSEARYTYSSAWFDAISAPPKLGRAAVSRGRLATVEQLPAKLRSEPLKFDAPWYRKSGTYRGKVQNLTQFYGFLQYQFVIPTEAVDEFKKIIGVIQASGHYSFLNVFKLFGPRNQAPLSFPIPGWNICVDFPIKDGLGKFVSELDRRVLEFGGRLYTAKDSRTTAETFHAMYPRVDEWISVRRKVDPLRVFASDMARRLELL 461
                                    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  ||   302       312 ||    338       348       358       368       378       388       398       408       418       428       438       448       458   
                                                                                                                                                                                                                                                                                                270|               314|                                                                                                                                  
                                                                                                                                                                                                                                                                                                 296                331
   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 4NCR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 23)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DPRE1_MYCTO | P9WJF0: 4fdn 4fdo 4fdp 4feh 4ff6 4p8c 4p8h 4p8k 4p8l 4p8m 4p8n 4p8p 4p8t 4p8y
        DPRE1_MYCTU | P9WJF1: 4fdn 4fdo 4fdp 4feh 4ff6 4kw5 4p8c 4p8h 4p8k 4p8l 4p8m 4p8n 4p8p 4p8t 4p8y 4pfa 4pfd

(-) Related Entries Specified in the PDB File

4f4q M. SMEGMATIS DPRE1 STRUCTURE IN COMPLEX WITH BTZ043
4fdp M. TUBERCULOSIS DPRE1 STRUCTURE