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(-) Description

Title :  CRYSTAL STRUCTURES OF MYCOBACTERIUM TUBERCULOSIS 6-OXOPURINE PHOSPHORIBOSYLTRANSFERASE WHICH IS A POTENTIAL TARGET FOR DRUG DEVELOPMENT AGAINST THIS DISEASE
 
Authors :  W. S. Eng, D. Hockova, P. Spacek, N. P. West, K. Woods, L. M. J. Naesens, D. L. W. Guddat
Date :  03 Oct 14  (Deposition) - 20 May 15  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  6-Oxopurine Phosphoribosyltransferase, Cytoplasmic, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. S. Eng, D. Hockova, P. Spacek, Z. Janeba, N. P. West, K. Woods, L. M. Naesens, D. T. Keough, L. W. Guddat
First Crystal Structures Of Mycobacterium Tuberculosis 6-Oxopurine Phosphoribosyltransferase: Complexes With Gmp And Pyrophosphate And With Acyclic Nucleoside Phosphonates Whose Prodrugs Have Antituberculosis Activity.
J. Med. Chem. V. 58 4822 2015
PubMed-ID: 25915781  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00611

(-) Compounds

Molecule 1 - HYPOXANTHINE-GUANINE PHOSPHORIBOSYLTRANSFERASE
    Chains: A, B, C, D
    Engineered: YES
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 419947
    Other Details: THIS SEQUENCE OCCURS NATURALLY IN MYCOBACTERIUM TUBERCULOSIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
13QG4Ligand/Ion[2-({2-[BIS(2-PHOSPHONOETHYL)AMINO]ETHYL}[2-(6-OXO-3,6-DIHYDRO-9H-PURIN-9-YL)ETHYL]AMINO)ETHYL]PHOSPHONICACID
2MG8Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
13QG4Ligand/Ion[2-({2-[BIS(2-PHOSPHONOETHYL)AMINO]ETHYL}[2-(6-OXO-3,6-DIHYDRO-9H-PURIN-9-YL)ETHYL]AMINO)ETHYL]PHOSPHONICACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
13QG2Ligand/Ion[2-({2-[BIS(2-PHOSPHONOETHYL)AMINO]ETHYL}[2-(6-OXO-3,6-DIHYDRO-9H-PURIN-9-YL)ETHYL]AMINO)ETHYL]PHOSPHONICACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
13QG2Ligand/Ion[2-({2-[BIS(2-PHOSPHONOETHYL)AMINO]ETHYL}[2-(6-OXO-3,6-DIHYDRO-9H-PURIN-9-YL)ETHYL]AMINO)ETHYL]PHOSPHONICACID
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:122 , ASP A:123 , HOH A:403 , HOH A:404 , HOH A:448 , HOH A:455BINDING SITE FOR RESIDUE MG A 301
02AC2SOFTWAREASP A:182 , 3QG A:303 , HOH A:401 , HOH A:402 , HOH A:405 , HOH A:447BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWARELEU A:65 , LYS A:66 , GLY A:67 , SER A:92 , VAL A:125 , ASP A:126 , SER A:127 , GLY A:128 , LEU A:129 , THR A:130 , LYS A:154 , PHE A:175 , VAL A:176 , LEU A:181 , ASP A:182 , ARG A:188 , MG A:302 , HOH A:402 , HOH A:403 , HOH A:404 , HOH A:406 , HOH A:408 , HOH A:449 , HOH A:450 , HOH A:451BINDING SITE FOR RESIDUE 3QG A 303
04AC4SOFTWAREGLU B:122 , ASP B:123 , HOH B:402 , HOH B:403 , HOH B:450 , HOH B:455BINDING SITE FOR RESIDUE MG B 301
05AC5SOFTWAREASP B:182 , 3QG B:303 , HOH B:401 , HOH B:404 , HOH B:405BINDING SITE FOR RESIDUE MG B 302
06AC6SOFTWARELEU B:65 , LYS B:66 , GLY B:67 , VAL B:125 , ASP B:126 , SER B:127 , GLY B:128 , LEU B:129 , THR B:130 , LYS B:154 , PHE B:175 , VAL B:176 , ASP B:182 , ARG B:188 , MG B:302 , HOH B:401 , HOH B:404 , HOH B:431 , HOH B:446 , HOH B:455BINDING SITE FOR RESIDUE 3QG B 303
07AC7SOFTWAREGLU C:122 , ASP C:123 , HOH C:401 , HOH C:402 , HOH C:403 , HOH C:446BINDING SITE FOR RESIDUE MG C 301
08AC8SOFTWAREASP C:182 , 3QG C:303 , HOH C:404 , HOH C:405 , HOH C:408 , HOH C:445BINDING SITE FOR RESIDUE MG C 302
09AC9SOFTWARELEU C:65 , LYS C:66 , GLY C:67 , SER C:92 , VAL C:125 , ASP C:126 , SER C:127 , GLY C:128 , LEU C:129 , THR C:130 , LYS C:154 , PHE C:175 , VAL C:176 , ASP C:182 , ARG C:188 , MG C:302 , HOH C:403 , HOH C:406 , HOH C:408 , HOH C:409BINDING SITE FOR RESIDUE 3QG C 303
10BC1SOFTWAREGLU D:122 , ASP D:123 , HOH D:401 , HOH D:402 , HOH D:403 , HOH D:407BINDING SITE FOR RESIDUE MG D 301
11BC2SOFTWAREASP D:182 , 3QG D:303 , HOH D:406 , HOH D:413 , HOH D:453 , HOH D:460BINDING SITE FOR RESIDUE MG D 302
12BC3SOFTWARELYS D:66 , GLY D:67 , SER D:92 , VAL D:124 , ASP D:126 , SER D:127 , GLY D:128 , LEU D:129 , THR D:130 , LYS D:154 , ASP D:174 , PHE D:175 , VAL D:176 , ASP D:182 , ARG D:188 , MG D:302 , HOH D:404 , HOH D:405 , HOH D:406 , HOH D:412 , HOH D:435 , HOH D:455BINDING SITE FOR RESIDUE 3QG D 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:65 -Lys A:66
2Leu B:65 -Lys B:66
3Leu C:65 -Lys C:66
4Leu D:65 -Lys D:66

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RHY)

(-) 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:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeehhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eeeeeeeee....eeee.........eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeee.hhhhhh.....eeeee.....ee...............eeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhy A  17 ELYPGDIKSVLLTAEQIQARIAELGEQIGNDYREGQDLLLITVLKGAVLFVTDLARAIPVPTQFEFMAVSSYVVRILKDLDRDIHGRDVLIVEDVVDSGLTLSWLSRNLTSRNPRSLRVCTLLRKPDAVHANVEIAYVGFDIPNDFVVGYGLDYDERYRDLSYIGTLDPRVY 201
                                    26        36        46   ||   61        71        81        91 ||    109       119       129       139       149       159       169       179       189       199  
                                                            50|                                   93|                                                                                                   
                                                             56                                   102                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:173
                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeehhhhhhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhhh...eeeeeeeeee....eeeee.........eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeee.hhhhhh.....eeeee.....ee...............eeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhy B  17 ELYPGDIKSVLLTAEQIQARIAELGEQIGNDYRGQDLLLITVLKGAVLFVTDLARAIPVPTQFEFMAVSSYGGVVRILKDLDRDIHGRDVLIVEDVVDSGLTLSWLSRNLTSRNPRSLRVCTLLRKPDAVHANVEIAYVGFDIPNDFVVGYGLDYDERYRDLSYIGTLDPRVY 201
                                    26        36        46  ||    62        72        82        92 ||    108       118       128       138       148       158       168       178       188       198   
                                                           49|                                    94|                                                                                                    
                                                            56                                    101                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eeeeeeeeee....eeeee.........eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeee.hhhh.......eeeee.....ee...............eeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhy C  17 ELYPGDIKSVLLTAEQIQARIAELGEQIGNDYRETTGQDLLLITVLKGAVLFVTDLARAIPVPTQFEFMAVSSYSGVVRILKDLDRDIHGRDVLIVEDVVDSGLTLSWLSRNLTSRNPRSLRVCTLLRKPDAVHANVEIAYVGFDIPNDFVVGYGLDYDERYRDLSYIGTLDPRVYQ 202
                                    26        36        46   ||   59        69        79        89   ||  105       115       125       135       145       155       165       175       185       195       
                                                            50|                                     93|                                                                                                      
                                                             54                                     100                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhhhhhhhhhhhhhhhh......eeeeee...hhhhhhhhhhhh...eeeeeeeeee......eeeee.........eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeee.hhhh.......eeeee.....ee...............eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rhy D  18 LYPGDIKSVLLTAEQIQARIAELGEQIGNDYRATTGQDLLLITVLKGAVLFVTDLARAIPVPTQFEFMAVSSYGSSGVVRILKDLDRDIHGRDVLIVEDVVDSGLTLSWLSRNLTSRNPRSLRVCTLLRKPDAVHANVEIAYVGFDIPNDFVVGYGLDYDERYRDLSYIGTLDPRVYQ 202
                                    27        37        47 ||     60        70        80        90    || 104       114       124       134       144       154       164       174       184       194        
                                                          49|                                        95|                                                                                                      
                                                           53                                        100
   Legend:   → Mismatch (orange background)
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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 4RHY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 20)

Asymmetric Unit(hide GO term definitions)

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  4rhy
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 Related Entries

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(-) Related Entries Specified in the PDB File

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