2LY7 - JenaLib

Title :   B-FLAP DOMAIN OF RNA POLYMERASE (B. SUBTILIS)

Authors :   M. Mobli

Date :   12 Sep 12 (Deposition) - 12 Mar 14 (Release) - 16 Dec 15 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)
NMR Structure *: A  (1x)

Keywords :   Rna Polymerase, Transcription, Non-Uniform Sampling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Ma, M. Mobli, X. Yang, A. N. Keller, G. F. King, P. J. Lewis
Rna Polymerase-Induced Remodelling Of Nusa Produces A Pause Enhancement Complex.
Nucleic Acids Res. V. 43 2829 2015
PubMed-ID: 25690895 | Reference-DOI: 10.1093/NAR/GKV108

Compounds

Molecule 1 - DNA-DIRECTED RNA POLYMERASE SUBUNIT BETA
	Chains	:	A
	EC Number	:	2.7.7.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	RPOB, CRSE, RFM, BSU01070
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	224308
	Strain	:	168
	Synonym	:	RNAP SUBUNIT BETA, RNA POLYMERASE SUBUNIT BETA, TRANSCRIPTASE SUBUNIT BETA

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

NMR Structure

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:139
 aligned with RPOB_BACSU | P37870 from UniProtKB/Swiss-Prot  Length:1193

    Alignment length:139
                                   794       804       814       824       834       844       854       864       874       884       894       904       914         
           RPOB_BACSU   785 DVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGIIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGD 923
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee..................................................eee......hhhhhhhhhhhh.....eee..........eeeeeeeeehhhhh.........eeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------RN PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ly7 A   3 DVYTSIHIEEYESEARDTKLGPEEITRDIPNVGEDALRNLDDRGVIRIGAEVKDGDLLVGKVTPKGVTELTAEERLLHAIFGEKAREVRDTSLRVPHGGGGIIHDVKVFNREDGDELPPGVNQLVRVYIVQKRKISEGD 141
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

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 (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

NMR Structure(hide GO term definitions)

Chain A (RPOB_BACSU | P37870)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003899	DNA-directed 5'-3' RNA polymerase activity	Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0032549	ribonucleoside binding	Interacting selectively and non-covalently with a ribonucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked to ribose.
	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.
biological process
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0000428	DNA-directed RNA polymerase complex	A protein complex that possesses DNA-directed RNA polymerase activity.

Visualization

Interactive Views

NMR Structure
	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
(no "Ligands, Modified Residues, Ions" information available for 2ly7)

	Sites
(no "Sites" information available for 2ly7)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2ly7)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2ly7
		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
	RPOB_BACSU \| P37870
		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)
	2.7.7.6
		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

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	RPOB_BACSU \| P37870
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description