1A4X - JenaLib

Title :   PYRR, THE BACILLUS SUBTILIS PYRIMIDINE BIOSYNTHETIC OPERON REPRESSOR, HEXAMERIC FORM

Authors :   D. R. Tomchick, R. J. Turner, R. W. Switzer, J. L. Smith

Date :   08 Feb 98 (Deposition) - 05 Aug 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym./Biol. Unit : A,B

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 Of 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
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS 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:201	BINDING SITE FOR RESIDUE SO4 A 184
2	AC2	SOFTWARE	LYS B:40 , ASP B:105 , VAL B:107 , LEU B:108 , TYR B:109 , THR B:110 , GLY B:111 , ARG B:112 , THR B:113 , VAL B:114 , HOH B:203	BINDING SITE FOR RESIDUE SO4 B 184
3	PRA	UNKNOWN	ASP 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:40	DUAL 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.
4	PRB	UNKNOWN	ASP 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:40	DUAL 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.

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:167
 aligned with PYRR_BACSU | P39765 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:177
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       
           PYRR_BACSU     4 KAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYEN 180
               SCOP domains d1a4xa_ A: Pyrimidine operon regulator PyrR                                                                                                                                       SCOP domains
               CATH domains 1a4xA00 A:4-180  [code=3.40.50.2020, no name defined]                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhhhh.hhh..eeeeee.hhhhhhhhhhhhhhhhhh.....eeee......----------......eee.......eeeeee......hhhhhhhhhhhhh....eeeeee..........................eeeee........eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a4x A   4 KAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYR----------EPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYEN 180
                                    13        23        33        43        53        63        73         -|       93       103       113       123       133       143       153       163       173       
                                                                                                73         84

Chain B from PDB  Type:PROTEIN  Length:167
 aligned with PYRR_BACSU | P39765 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:177
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       
           PYRR_BACSU     4 KAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLYRDDLSKKTSNDEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYEN 180
               SCOP domains d1a4xb_ B: Pyrimidine operon regulator PyrR                                                                                                                                       SCOP domains
               CATH domains 1a4xB00 B:4-180  [code=3.40.50.2020, no name defined]                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhhhh.hhh..eeeeee.hhhhhhhhhhhhhhhhhh.....eeeeee...----------....eeeeee.......eeeeee......hhhhhhhhhhhhh....eeeeee..........................eeeee........eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1a4x B   4 KAVILDEQAIRRALTRIAHEMIERNKGMNNCILVGIKTRGIYLAKRLAERIEQIEGNPVTVGEIDITLY----------DEPLVKGADIPVDITDQKVILVDDVLYTGRTVRAGMDALVDVGRPSSIQLAVLVDRGHRELPIRADYIGKNIPTSKSEKVMVQLDEVDQNDLVAIYEN 180
                                    13        23        33        43        53        63        |-        83        93       103       113       123       133       143       153       163       173       
                                                                                               72         83

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)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		PRA	[ RasMol ]	+environment [ RasMol ]
		PRB	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1a4x)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1a4x
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PYRR_BACSU \| P39765
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description