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(-) Description

Title :  PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, DIMERIC FORM
 
Authors :  D. R. Tomchick, R. J. Turner, R. W. Switzer, J. L. Smith
Date :  20 Jan 98  (Deposition) - 05 Aug 98  (Release) - 16 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transcription Regulation, Attenuation Protein, Rna-Binding Protein, Pyrimidine Biosynthesis, Transferase, Prtase, Phosphoribosyltransferase, Bifunctional Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. R. Tomchick, R. J. Turner, R. L. Switzer, J. L. Smith
Adaptation Of An Enzyme To Regulatory Function: Structure O Bacillus Subtilis Pyrr, A Pyr Rna-Binding Attenuation Protein And Uracil Phosphoribosyltransferase.
Structure V. 6 337 1998
PubMed-ID: 9551555  |  Reference-DOI: 10.1016/S0969-2126(98)00036-7

(-) Compounds

Molecule 1 - PYRIMIDINE OPERON REGULATORY PROTEIN PYRR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTSROX3
    Expression System Strain: S0408
    Expression System Taxid: 562
    Gene: PYRR
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Synonym: PYRR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1SM2Ligand/IonSAMARIUM (III) ION
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SM-1Ligand/IonSAMARIUM (III) ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:10 , ASP A:167 , ASP A:173BINDING SITE FOR RESIDUE SM A 182
2AC2SOFTWAREHOH A:325 , HOH A:335BINDING SITE FOR RESIDUE SM A 183
3AC3SOFTWARELYS A:40 , ASP A:105 , VAL A:107 , LEU A:108 , TYR A:109 , THR A:110 , GLY A:111 , ARG A:112 , THR A:113 , VAL A:114 , HOH A:261BINDING SITE FOR RESIDUE SO4 A 184
4PRAUNKNOWNASP A:105 , ASP A:106 , VAL A:107 , LEU A:108 , TYR A:109 , THR A:110 , GLY A:111 , ARG A:112 , THR A:113 , LYS A:40DUAL SITE: BINDING SITE FOR SUBSTRATE PRPP IN THIS AND OTHER MEMBERS OF THE TYPE I PHOSPHORIBOSYLTRANSFERASE (PRTASE) FAMILY OF ENZYMES, AND SULFATE ION BINDING SITE.
5SM1UNKNOWNSM A:182 , GLU A:10 , ASP A:167 , ASP A:173SM3+ ION BINDING SITE. THE SM3+ ION LIES ON A CRYSTALLOGRAPHIC TWO-FOLD AXIS, AND ISOCTAHEDRALLY COORDINATED BY THE OXYGENS OF THREE AMINO ACID SIDE CHAINS AND THEIR SYMMETRY RELATED ATOMS.
6SM2UNKNOWNSM A:183SM3+ ION BINDING SITE. THE SM3+ ION LIES ON A GENERAL POSITION AND IS COORDINATED BY WATERS.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1A3C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1A3C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1A3C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1A3C)

(-) Exons   (0, 0)

(no "Exon" information available for 1A3C)

(-) 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:166
 aligned with PYRR_BACSU | P39765 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:178
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172        
           PYRR_BACSU     3 QKAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYEN 180
               SCOP domains d1a3ca_ A: Pyrimidine opero    n regulator PyrR                                                                                                                                    SCOP domains
               CATH domains 1a3cA00 A:3-180  [code=3.40    .50.2020, no name defined]                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.hhhhhhhhhhhhhhhhhh..----.eeeee.hhhhhhhhhhhhhhhhhh....eeeeeeee...--------....eeeeee........eeeeee......hhhhhhhhhhhhh....eeeeee..........................eeeee.hhhh...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a3c A   3 QKAVILDEQAIRRALTRIAHEMIERNK----CILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYR--------NDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYEN 180
                                    12        22      |  - |      42        52        62        72|       82        92       102       112       122       132       142       152       162       172        
                                                     29   34                                     73       82
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1A3C)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (PYRR_BACSU | P39765)
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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  1a3c
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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRR_BACSU | P39765: 1a4x 4p82

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