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NMR Structure - model 1 (Jmol Viewer)

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Title :   NMR SOLUTION STRUCTURE OF THE DNA BINDING DOMAIN OF COMPETENCE PROTEIN A

Authors :   C. A. Hobbs, B. G. Bobay, R. J. Thompson, M. Perego, J. Cavanagh

Date :   16 Dec 09 (Deposition) - 07 Apr 10 (Release) - 05 May 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (10x)
NMR Structure *: A,B  (1x)

Keywords :   Activator, Competence, Dna-Binding, Transcription Regulation, Two- Component Regulatory System, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. A. Hobbs, B. G. Bobay, R. J. Thompson, M. Perego, J. Cavanagh
Nmr Solution Structure And Dna-Binding Model Of The Dna-Binding Domain Of Competence Protein A.
J. Mol. Biol. V. 398 248 2010
PubMed-ID: 20302877 | Reference-DOI: 10.1016/J.JMB.2010.03.003

Molecule 1 - TRANSCRIPTIONAL REGULATORY PROTEIN COMA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 146-214
	Gene	:	BSU31680, COMA, COMA1, COMAA
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2
NMR Structure (10x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2KRF)

(no "Site" information available for 2KRF)

(no "SS Bond" information available for 2KRF)

(no "Cis Peptide Bond" information available for 2KRF)

(no "SAP(SNP)/Variant" information available for 2KRF)

NMR Structure (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_2	PS50043	LuxR-type HTH domain profile.	CMPA_BACSU	147-212	2	A:147-212 B:147-212
2	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	CMPA_BACSU	168-195	2	A:168-195 B:168-195

NMR Structure * (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_LUXR_2	PS50043	LuxR-type HTH domain profile.	CMPA_BACSU	147-212	2	A:147-212 B:147-212
2	HTH_LUXR_1	PS00622	LuxR-type HTH domain signature.	CMPA_BACSU	168-195	2	A:168-195 B:168-195

(no "Exon" information available for 2KRF)

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
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Chain A from PDB  Type:PROTEIN  Length:69
 aligned with CMPA_BACSU | P14204 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:69
                                   155       165       175       185       195       205         
           CMPA_BACSU   146 SSQKEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGVL 214
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains 2krfA00 A:146-214 'winged helix' repressor DNA binding domain         CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_LUXR_2  PDB: A:147-212 UniProt: 147-212                       -- PROSITE (1)
                PROSITE (2) ----------------------HTH_LUXR_1  PDB: A:168-195  ------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------- Transcript
                 2krf A 146 SSQKEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGVL 214
                                   155       165       175       185       195       205

Chain B from PDB  Type:PROTEIN  Length:69
 aligned with CMPA_BACSU | P14204 from UniProtKB/Swiss-Prot  Length:214

    Alignment length:69
                                   155       165       175       185       195       205         
           CMPA_BACSU   146 SSQKEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGVL 214
               SCOP domains --------------------------------------------------------------------- SCOP domains
               CATH domains 2krfB00 B:146-214 'winged helix' repressor DNA binding domain         CATH domains
           Pfam domains (1) -----GerE-2krfB01 B:151-208                                    ------ Pfam domains (1)
           Pfam domains (2) -----GerE-2krfB02 B:151-208                                    ------ Pfam domains (2)
         Sec.struct. author .........hhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_LUXR_2  PDB: B:147-212 UniProt: 147-212                       -- PROSITE (1)
                PROSITE (2) ----------------------HTH_LUXR_1  PDB: B:168-195  ------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------- Transcript
                 2krf B 146 SSQKEQDVLTPRECLILQEVEKGFTNQEIADALHLSKRSIEYSLTSIFNKLNVGSRTEAVLIAKSDGVL 214
                                   155       165       175       185       195       205

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 '\|'

(no "SCOP Domain" information available for 2KRF)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: 'winged helix' repressor DNA binding domain (507)

Bacillus subtilis. Organism_taxid: 1423. (15)

1a	2krfA00	A:146-214
1b	2krfB00	B:146-214

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: GerE (15)

Bacillus subtilis (1)

1a	GerE-2krfB01	B:151-208
1b	GerE-2krfB02	B:151-208

NMR Structure(hide GO term definitions)

Chain A,B (CMPA_BACSU | P14204)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0030420	establishment of competence for transformation	The process in which a naturally transformable bacterium acquires the ability to take up exogenous DNA. This term should be applied only to naturally transformable bacteria, and should not be used in the context of artificially induced bacterial transformation.
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

NMR Structure
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