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(-) Description

Title :  PYRR OF MYCOBACTERIUM TUBERCULOSIS AS A POTENTIAL DRUG TARGET
 
Authors :  K. A. Kantardjieff, C. Vasquez, P. Castro, N. N. Warfel, B. -S. Rho, T. Lekin, C. -Y. Kim, B. W. Segelke, T. Terwilliger, B. Rupp, Tb Structural Genomics Consortium (Tbsgc)
Date :  11 Jul 04  (Deposition) - 29 Sep 04  (Release) - 06 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Pyrr, Transferase, Glycosyltransferase, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tb, Tbsgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. A. Kantardjieff, C. Vasquez, P. Castro, N. N. Warfel, B. -S. Rho, T. Lekin, C. -Y. Kim, B. W. Segelke, T. Terwilliger, B. Rupp
Structure Of Pyrr (Rv1379) From Mycobacterium Tuberculosis: A Persistence Gene And Protein Drug Target
Acta Crystallogr. , Sect. D V. 61 355 2005
PubMed-ID: 15805589  |  Reference-DOI: 10.1107/S090744490403389X

(-) Compounds

Molecule 1 - PYRR BIFUNCTIONAL PROTEIN
    ChainsA, B
    EC Number2.4.2.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET
    MutationYES
    Organism ScientificMYCOBACTERIUM TUBERCULOSIS
    Organism Taxid1773
    Other DetailsGSHHHHHH C-TERMINAL TAG
    StrainHRV37
    SynonymURACIL PHOSPHORIBOSYLTRANSFERASE, UPRTASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1W30)

(-) Sites  (0, 0)

(no "Site" information available for 1W30)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W30)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:56 -Thr A:57
2Pro B:56 -Thr B:57

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W30)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W30)

(-) Exons   (0, 0)

(no "Exon" information available for 1W30)

(-) 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:174
 aligned with PYRR_MYCBO | P65942 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:182
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           PYRR_MYCBO    12 ESRELMSAADVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRDDLMIKPPRPLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
               SCOP domains d1w30a_ A: Pyrimidine operon regulator PyrR                                                                                                                                            SCOP domains
               CATH domains 1w30A00 A:12-193  [code=3.40.50.2020, no name defined]                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhh.--------...............eeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeee...........eeeee.......eeeeehhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w30 A  12 ESRELMSAANVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRD--------PLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
                                    21        31        41        51        61        71        81        |-       101       111       121       131       141       151       161       171       181       191  
                                                                                                         90       99                                                                                              

Chain A from PDB  Type:PROTEIN  Length:174
 aligned with PYRR_MYCTO | P9WHK2 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:182
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           PYRR_MYCTO    12 ESRELMSAADVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRDDLMIKPPRPLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
               SCOP domains d1w30a_ A: Pyrimidine operon regulator PyrR                                                                                                                                            SCOP domains
               CATH domains 1w30A00 A:12-193  [code=3.40.50.2020, no name defined]                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhh.--------...............eeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeee...........eeeee.......eeeeehhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w30 A  12 ESRELMSAANVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRD--------PLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
                                    21        31        41        51        61        71        81        |-       101       111       121       131       141       151       161       171       181       191  
                                                                                                         90       99                                                                                              

Chain A from PDB  Type:PROTEIN  Length:174
 aligned with PYRR_MYCTU | P9WHK3 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:182
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           PYRR_MYCTU    12 ESRELMSAADVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRDDLMIKPPRPLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
               SCOP domains d1w30a_ A: Pyrimidine operon regulator PyrR                                                                                                                                            SCOP domains
               CATH domains 1w30A00 A:12-193  [code=3.40.50.2020, no name defined]                                                                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhhhhh............eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhh.--------...............eeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeee...........eeeee.......eeeeehhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w30 A  12 ESRELMSAANVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRD--------PLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
                                    21        31        41        51        61        71        81        |-       101       111       121       131       141       151       161       171       181       191  
                                                                                                         90       99                                                                                              

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with PYRR_MYCBO | P65942 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:182
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           PYRR_MYCBO    12 ESRELMSAADVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRDDLMIKPPRPLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
               SCOP domains d1w30b_ B: Pyrimidine operon regulator PyrR                                                                                                                                            SCOP domains
               CATH domains 1w30B00 B:12-193  [code=3.40.50.2020, no name defined]                                                                                                                                 CATH domains
           Pfam domains (1) --Pribosyltran-1w30B01 B:14-150                                                                                                            ------------------------------------------- Pfam domains (1)
           Pfam domains (2) --Pribosyltran-1w30B02 B:14-150                                                                                                            ------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhhhhhh...........eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhh.-----..................eeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeee...........eeeee.......eeeeehhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w30 B  12 ESRELMSAANVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRD-----PPRPLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
                                    21        31        41        51        61        71        81        |-    |  101       111       121       131       141       151       161       171       181       191  
                                                                                                         90    96                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with PYRR_MYCTO | P9WHK2 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:182
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           PYRR_MYCTO    12 ESRELMSAADVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRDDLMIKPPRPLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
               SCOP domains d1w30b_ B: Pyrimidine operon regulator PyrR                                                                                                                                            SCOP domains
               CATH domains 1w30B00 B:12-193  [code=3.40.50.2020, no name defined]                                                                                                                                 CATH domains
           Pfam domains (1) --Pribosyltran-1w30B01 B:14-150                                                                                                            ------------------------------------------- Pfam domains (1)
           Pfam domains (2) --Pribosyltran-1w30B02 B:14-150                                                                                                            ------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhhhhhh...........eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhh.-----..................eeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeee...........eeeee.......eeeeehhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w30 B  12 ESRELMSAANVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRD-----PPRPLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
                                    21        31        41        51        61        71        81        |-    |  101       111       121       131       141       151       161       171       181       191  
                                                                                                         90    96                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:177
 aligned with PYRR_MYCTU | P9WHK3 from UniProtKB/Swiss-Prot  Length:193

    Alignment length:182
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  
           PYRR_MYCTU    12 ESRELMSAADVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRDDLMIKPPRPLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
               SCOP domains d1w30b_ B: Pyrimidine operon regulator PyrR                                                                                                                                            SCOP domains
               CATH domains 1w30B00 B:12-193  [code=3.40.50.2020, no name defined]                                                                                                                                 CATH domains
           Pfam domains (1) --Pribosyltran-1w30B01 B:14-150                                                                                                            ------------------------------------------- Pfam domains (1)
           Pfam domains (2) --Pribosyltran-1w30B02 B:14-150                                                                                                            ------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeehhhhhhhhhhhhhhhhhhhhh...........eeeee..hhhhhhhhhhhhhhhhhhh...eeee..hhhhh.-----..................eeeeeeeee..hhhhhhhhhhhhhhh...eeeeeeeee...........eeeee.......eeeeehhhhhh..eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w30 B  12 ESRELMSAANVGRTISRIAHQIIEKTALDDPVGPDAPRVVLLGIPTRGVTLANRLAGNITEYSGIHVGHGALDITLYRD-----PPRPLASTSIPAGGIDDALVILVDDVLYSGRSVRSALDALRDVGRPRAVQLAVLVDRGHRELPLRADYVGKNVPTSRSESVHVRLREHDGRDGVVISR 193
                                    21        31        41        51        61        71        81        |-    |  101       111       121       131       141       151       161       171       181       191  
                                                                                                         90    96                                                                                                 

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (7, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PYRR_MYCBO | P65942)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0004845    uracil phosphoribosyltransferase activity    Catalysis of the reaction: diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil.
biological process
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain A,B   (PYRR_MYCTO | P9WHK2)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0004845    uracil phosphoribosyltransferase activity    Catalysis of the reaction: diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil.
biological process
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain A,B   (PYRR_MYCTU | P9WHK3)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0004845    uracil phosphoribosyltransferase activity    Catalysis of the reaction: diphosphate + UMP = 5-phospho-alpha-D-ribose 1-diphosphate + uracil.
biological process
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.

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 Related Entries

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

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        PYRR_MYCTU | P9WHK35iao

(-) Related Entries Specified in the PDB File

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