P74565 (RPOD_SYNY3) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
RNA polymerase sigma factor RpoD

Gene names

Name:	rpoD
Synonyms:	rpoD1
Ordered Locus Names:	slr0653

Organism

Synechocystis sp. (strain PCC 6803 / Kazusa) [Reference proteome] [HAMAP]

Taxonomic identifier

1111708 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Cyanobacteria › Oscillatoriophycideae › Chroococcales › Synechocystis › Synechocystis sp. PCC 6803

Protein attributes

Sequence length	425 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.
Sequence similarities	Belongs to the sigma-70 factor family.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Ligand	DNA-binding
Molecular function	Sigma factor
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA-dependent transcription, initiation Inferred from electronic annotation. Source: InterPro
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW sequence-specific DNA binding transcription factor activity Inferred from electronic annotation. Source: InterPro sigma factor activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 425	425	RNA polymerase sigma factor RpoD		PRO_0000093928
Regions
	DNA binding	386 – 405	20	H-T-H motif By similarity
	Motif	217 – 230	14	Polymerase core binding Potential

Sequences

	Sequence		Length	Mass (Da)
	P74565 [UniParc]. Last modified February 1, 1997. Version 1. Checksum: 4043FEA859B442D7	FASTA	425	49,936
	10 20 30 40 50 60 MTQTKEPLTK AESAELEQEI ELSQYINTDD IDDDDIDVED LEQEVAATEG KEKKVRKIRK 70 80 90 100 110 120 DAVKKKPYTE DSIRIYLQEI GRIRLLRAEE EIELARQIAD LLELELIRDN LTLQLERQPS 130 140 150 160 170 180 ELEWGKQVWK LETAKQRLVG DKKKEPKKKD IDSYLANPDN ELSLENEWSQ QPNKNFAAFR 190 200 210 220 230 240 RRLFLDRRAK DKMVQSNLRL VVSIAKKYMN RGLSFQDLIQ EGSLGLIRAA EKFDHEKGYK 250 260 270 280 290 300 FSTYATWWIR QAITRAIADQ SRTIRLPVHL YETISRIKKT TKLLSQEMRR KPTEEEIAEK 310 320 330 340 350 360 MEMTIEKLRF IAKSAQLPIS LETPIGKEED SRLGDFIEAD GETPEDEVSK NLLREDLENV 370 380 390 400 410 420 LDTLSPRERD VLRLRYGLDD GRMKTLEEIG QIFNVTRERI RQIEAKALRK LRHPNRNSIL KEYIR

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions." Kaneko T., Sato S., Kotani H., Tanaka A., Asamizu E., Nakamura Y., Miyajima N., Hirosawa M., Sugiura M., Sasamoto S., Kimura T., Hosouchi T., Matsuno A., Muraki A., Nakazaki N., Naruo K., Okumura S., Shimpo S. , Takeuchi C., Wada T., Watanabe A., Yamada M., Yasuda M., Tabata S. DNA Res. 3:109-136(1996) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: PCC 6803 / Kazusa.
[2]	"A new set of PCR primers for specific detection of the gene encoding the principal sigma factor in cyanobacteria." Asayama M., Yamada A., Tanaka K., Takahashi H., Shirai M. J. Gen. Appl. Microbiol. 42:511-515(1996) Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 211-396. Strain: 559.

Cross-references

Sequence databases
EMBL GenBank DDBJ	BA000022 Genomic DNA. Translation: BAA18672.1. D86213 Genomic DNA. Translation: BAA13043.1.
PIR	S76760.
RefSeq	NP_442860.1. NC_000911.1. YP_005652921.1. NC_017277.1. YP_007452736.1. NC_020286.1.
3D structure databases
ProteinModelPortal	P74565.
SMR	P74565. Positions 187-260, 347-424.
ModBase	Search...
Protein-protein interaction databases
IntAct	P74565. 42 interactions.
STRING	1148.slr0653.
Proteomic databases
PaxDb	P74565.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblBacteria	BAA18672; BAA18672; BAA18672.
GeneID	12255281. 14618421. 953190.
KEGG	syn:slr0653. syy:SYNGTS_2968.
PATRIC	23843506. VBISynSp132158_3288.
Phylogenomic databases
eggNOG	COG0568.
HOGENOM	HOG000270273.
KO	K03086.
OMA	HPNRNGV.
ProtClustDB	PRK07406.
Family and domain databases
Gene3D	1.10.10.10. 2 hits.
InterPro	IPR014284. RNA_pol_sigma-70_dom. IPR000943. RNA_pol_sigma70. IPR009042. RNA_pol_sigma70_r1_2. IPR007627. RNA_pol_sigma70_r2. IPR007624. RNA_pol_sigma70_r3. IPR007630. RNA_pol_sigma70_r4. IPR013325. RNA_pol_sigma_r2. IPR013324. RNA_pol_sigma_r3_r4. IPR012760. RNA_pol_sigma_RpoD_C. IPR017848. RNA_pol_sigma_RpoD_cyanobac. IPR011991. WHTH_DNA-bd_dom. [Graphical view]
Pfam	PF00140. Sigma70_r1_2. 1 hit. PF04542. Sigma70_r2. 1 hit. PF04539. Sigma70_r3. 1 hit. PF04545. Sigma70_r4. 1 hit. [Graphical view]
PRINTS	PR00046. SIGMA70FCT.
SUPFAM	SSF88946. Sigma_r2. 1 hit. SSF88659. Sigma_r3_r4. 2 hits.
TIGRFAMs	TIGR02393. RpoD_Cterm. 1 hit. TIGR02997. Sig70-cyanoRpoD. 1 hit. TIGR02937. sigma70-ECF. 1 hit.
PROSITE	PS00715. SIGMA70_1. 1 hit. PS00716. SIGMA70_2. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

RPOD_SYNY3

Accession

Primary (citable) accession number: P74565
Secondary accession number(s): Q55351

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 24, 2004
Last sequence update:	February 1, 1997
Last modified:	May 1, 2013
This is version 88 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program