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(-) Description

Title :  PYRR, THE REGULATOR OF THE PYRIMIDINE BIOSYNTHETIC OPERON IN BACILLUS CALDOLYTICUS
 
Authors :  R. L. Switzer, P. Chander, J. L. Smith, K. M. Halbig, J. K. Miller, H. K. Bonner, G. K. Grabner
Date :  16 Jan 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription Regulation; Attenuation Protein; Rna-Binding Protein; Pyrimidine Biosynthesis; Transferase; Prtase; Uracil Phosphoribosyltransferase; Bifunctional Enzyme, Transcription, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Chander, K. M. Halbig, J. K. Miller, C. J. Fields, H. K. Bonner, G. K. Grabner, R. L. Switzer, J. L. Smith
Structure Of The Nucleotide Complex Of Pyrr, The Pyr Attenuation Protein From Bacillus Caldolyticus, Suggests Dual Regulation By Pyrimidine And Purine Nucleotides
J. Bacteriol. V. 187 1773 2005
PubMed-ID: 15716449  |  Reference-DOI: 10.1128/JB.187.5.1773-1782.2005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PYRR BIFUNCTIONAL PROTEIN
    Chains: A, B, C, D
    EC Number: 2.4.2.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSHCO2
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PYRR
    Organism Scientific: BACILLUS CALDOLYTICUS
    Organism Taxid: 1394
    Other Details: INCLUDES PYRIMIDINE OPERON REGULATORY PROTEIN AND URACIL PHOSPHORIBOSYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1NON)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NON)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NON)

(-) 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:161
 aligned with PYRR_BACCL | P41007 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
           PYRR_BACCL     1 MQKAVVMDEQAIRRALTRIAHEIIERNKGIDGCVLVGIKTRGIYLARRLAERIEQIEGASVPVGELDITLYRDDLTVKTDDHEPLVKGTNVPFPVTERNVILVDDVLFTGRTVRAAMDAVMDLGRPARIQLAVLVDRGHRELPIRADFVGKNVPTSRSELIVVELSEVDGIDQVSIHEK 179
               SCOP domains d1nona_ A: Pyrimidine operon regulator PyrR                                                                                                                                         SCOP domains
               CATH domains 1nonA00 A:1-179  [code=3.40.50.2020, no name defined]                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhhhhh....eee.......------------------........eeeeeeeee..hhhhhhhhhhhhh.....eeeeeeeee...........eeeee.......eeeeehhhhhh..eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1non A   1 MQKAVVMDEQAIRRALTRIAHEIIERNKGIDGCVLVGIKTRGIYLARRLAERIEQIEGASVPVGELDITLYR------------------VPFPVTERNVILVDDVLFTGRTVRAAMDAVMDLGRPARIQLAVLVDRGHRELPIRADFVGKNVPTSRSELIVVELSEVDGIDQVSIHEK 179
                                    10        20        30        40        50        60        70 |       -         -|      100       110       120       130       140       150       160       170         
                                                                                                  72                 91                                                                                        


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with PYRR_BACCL | P41007 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
           PYRR_BACCL     1 MQKAVVMDEQAIRRALTRIAHEIIERNKGIDGCVLVGIKTRGIYLARRLAERIEQIEGASVPVGELDITLYRDDLTVKTDDHEPLVKGTNVPFPVTERNVILVDDVLFTGRTVRAAMDAVMDLGRPARIQLAVLVDRGHRELPIRADFVGKNVPTSRSELIVVELSEVDGIDQVSIHEK 179
               SCOP domains d1nonb_ B: Pyrimidine operon regulator PyrR                                                                                                                                         SCOP domains
               CATH domains 1nonB00 B:1-179  [code=3.40.50.2020, no name defined]                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh....eeee......------------------........eeeeeeeee..hhhhhhhhhhhh......eeeeeeeee...........eeeee.......eeeeehhhhhh..eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1non B   1 MQKAVVMDEQAIRRALTRIAHEIIERNKGIDGCVLVGIKTRGIYLARRLAERIEQIEGASVPVGELDITLYR------------------VPFPVTERNVILVDDVLFTGRTVRAAMDAVMDLGRPARIQLAVLVDRGHRELPIRADFVGKNVPTSRSELIVVELSEVDGIDQVSIHEK 179
                                    10        20        30        40        50        60        70 |       -         -|      100       110       120       130       140       150       160       170         
                                                                                                  72                 91                                                                                        


Chain C from PDB  Type:PROTEIN  Length:161
 aligned with PYRR_BACCL | P41007 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
           PYRR_BACCL     1 MQKAVVMDEQAIRRALTRIAHEIIERNKGIDGCVLVGIKTRGIYLARRLAERIEQIEGASVPVGELDITLYRDDLTVKTDDHEPLVKGTNVPFPVTERNVILVDDVLFTGRTVRAAMDAVMDLGRPARIQLAVLVDRGHRELPIRADFVGKNVPTSRSELIVVELSEVDGIDQVSIHEK 179
               SCOP domains d1nonc_ C: Pyrimidine operon regulator PyrR                                                                                                                                         SCOP domains
               CATH domains 1nonC00 C:1-179  [code=3.40.50.2020, no name defined]                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhh....eeee.hhhhh------------------........eeeeeeeee..hhhhhhhhhhhhh.....eeeeeeeee...........eeeee.......eeeeehhhhhh..eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1non C   1 MQKAVVMDEQAIRRALTRIAHEIIERNKGIDGCVLVGIKTRGIYLARRLAERIEQIEGASVPVGELDITLYR------------------VPFPVTERNVILVDDVLFTGRTVRAAMDAVMDLGRPARIQLAVLVDRGHRELPIRADFVGKNVPTSRSELIVVELSEVDGIDQVSIHEK 179
                                    10        20        30        40        50        60        70 |       -         -|      100       110       120       130       140       150       160       170         
                                                                                                  72                 91                                                                                        


Chain D from PDB  Type:PROTEIN  Length:161
 aligned with PYRR_BACCL | P41007 from UniProtKB/Swiss-Prot  Length:179

    Alignment length:179
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170         
           PYRR_BACCL     1 MQKAVVMDEQAIRRALTRIAHEIIERNKGIDGCVLVGIKTRGIYLARRLAERIEQIEGASVPVGELDITLYRDDLTVKTDDHEPLVKGTNVPFPVTERNVILVDDVLFTGRTVRAAMDAVMDLGRPARIQLAVLVDRGHRELPIRADFVGKNVPTSRSELIVVELSEVDGIDQVSIHEK 179
               SCOP domains d1nond_ D: Pyrimidine operon regulator PyrR                                                                                                                                         SCOP domains
               CATH domains 1nonD00 D:1-179  [code=3.40.50.2020, no name defined]                                                                                                                               CATH domains
           Pfam domains (1) --Pribosyltran-1nonD01 D:3-135                                                                                                         -------------------------------------------- Pfam domains (1)
           Pfam domains (2) --Pribosyltran-1nonD02 D:3-135                                                                                                         -------------------------------------------- Pfam domains (2)
           Pfam domains (3) --Pribosyltran-1nonD03 D:3-135                                                                                                         -------------------------------------------- Pfam domains (3)
           Pfam domains (4) --Pribosyltran-1nonD04 D:3-135                                                                                                         -------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeeehhhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhhhh....eeee......------------------........eeeeeeeee..hhhhhhhhhhhh......eeeeeeeee...........eeeee.......eeeeehhhhhh..eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1non D   1 MQKAVVMDEQAIRRALTRIAHEIIERNKGIDGCVLVGIKTRGIYLARRLAERIEQIEGASVPVGELDITLYR------------------VPFPVTERNVILVDDVLFTGRTVRAAMDAVMDLGRPARIQLAVLVDRGHRELPIRADFVGKNVPTSRSELIVVELSEVDGIDQVSIHEK 179
                                    10        20        30        40        50        60        70 |       -         -|      100       110       120       130       140       150       160       170         
                                                                                                  72                 91
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: PRTase-like (59)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (PYRR_BACCL | P41007)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0006353    DNA-templated transcription, termination    The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
    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.

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  1non
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRR_BACCL | P41007: 1xz8 1xzn 2igb

(-) Related Entries Specified in the PDB File

1a3c PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, DIMERIC FORM