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Protein

RNA polymerase sigma factor SigA

Gene

sigA

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.UniRule annotation

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi353 – 372H-T-H motifUniRule annotationAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Sigma factor
Biological processTranscription, Transcription regulation

Enzyme and pathway databases

BioCyciTMAR243274:G1H0Q-1412-MONOMER

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor SigAUniRule annotation
Alternative name(s):
Sigma-A
Gene namesi
Name:sigAUniRule annotation
Synonyms:rpoD
Ordered Locus Names:TM_1451
OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Taxonomic identifieri243274 [NCBI]
Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
Proteomesi
  • UP000008183 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000939291 – 399RNA polymerase sigma factor SigAAdd BLAST399

Proteomic databases

PRIDEiP77994

Interactioni

Subunit structurei

Interacts transiently with the RNA polymerase catalytic core.UniRule annotation

Protein-protein interaction databases

STRINGi243274.TM1451

Structurei

Secondary structure

1399
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi29 – 45Combined sources17
Helixi50 – 56Combined sources7
Helixi66 – 77Combined sources12
Beta strandi92 – 94Combined sources3
Helixi323 – 328Combined sources6
Helixi333 – 343Combined sources11
Turni344 – 347Combined sources4
Helixi353 – 359Combined sources7
Helixi364 – 378Combined sources15
Beta strandi382 – 384Combined sources3
Helixi385 – 393Combined sources9
Turni394 – 396Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TTYNMR-A313-399[»]
2K6XNMR-A29-96[»]
ProteinModelPortaliP77994
SMRiP77994
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP77994

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni30 – 107Sigma-70 factor domain-1Add BLAST78
Regioni159 – 229Sigma-70 factor domain-2Add BLAST71
Regioni238 – 313Sigma-70 factor domain-3Add BLAST76
Regioni327 – 380Sigma-70 factor domain-4Add BLAST54

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi183 – 186Interaction with polymerase core subunit RpoC4

Domaini

Contains 4 domains, connected by flexible linkers. In the active conformation, the domains are in an extended conformation, each making extensive interactions with the RNA polymerase catalytic core (PubMed:18940669).1 Publication
In the autoinhibited state, sigma-70 factor domain-1 packs closely together with sigma-70 factor domains-2 and -4, contrary to the extended conformation that is seen when the protein is part of the RNA polymerase holoenzyme.1 Publication
The sigma-70 factor domain-2 mediates sequence-specific interaction with the -10 element in promoter DNA, and plays an important role in melting the double-stranded DNA and the formation of the transcription bubble. The sigma-70 factor domain-2 mediates interaction with the RNA polymerase subunits RpoB and RpoC (By similarity).By similarity
The sigma-70 factor domain-4 contains a helix-turn-helix (H-T-H) motif that mediates interaction with the -35 element in promoter DNA. The domain also mediates interaction with the RNA polymerase subunit RpoA. Interactions between sigma-70 factor domain-4 and anti-sigma factors prevents interaction of sigma factors with the RNA polymerase catalytic core (By similarity).By similarity

Sequence similaritiesi

Belongs to the sigma-70 factor family. RpoD/SigA subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105DG1 Bacteria
COG0568 LUCA
InParanoidiP77994
KOiK03086
OMAiYQRWLAE

Family and domain databases

Gene3Di1.10.10.10, 2 hits
HAMAPiMF_00963 Sigma70_RpoD_SigA, 1 hit
InterProiView protein in 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
IPR007127 RNA_pol_sigma_70_r1_1
IPR013325 RNA_pol_sigma_r2
IPR013324 RNA_pol_sigma_r3/r4-like
IPR012760 RNA_pol_sigma_RpoD_C
IPR028630 Sigma70_RpoD
IPR036388 WH-like_DNA-bd_sf
PfamiView protein in Pfam
PF03979 Sigma70_r1_1, 1 hit
PF00140 Sigma70_r1_2, 1 hit
PF04542 Sigma70_r2, 1 hit
PF04539 Sigma70_r3, 1 hit
PF04545 Sigma70_r4, 1 hit
PRINTSiPR00046 SIGMA70FCT
SUPFAMiSSF88659 SSF88659, 2 hits
SSF88946 SSF88946, 1 hit
TIGRFAMsiTIGR02393 RpoD_Cterm, 1 hit
TIGR02937 sigma70-ECF, 1 hit
PROSITEiView protein in PROSITE
PS00715 SIGMA70_1, 1 hit
PS00716 SIGMA70_2, 1 hit

Sequencei

Sequence statusi: Complete.

P77994-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNEEQQVLQE QHQEQTQEQT QEQKETLPPQ IERRIKKLIS LGKKKGYITY
60 70 80 90 100
EDIDKAFPPD FEGFDTNLIE RIHEELEKHG INIVENEPEE EEISASSDEQ
110 120 130 140 150
ELEELLEKES PEIHDSSNVR DSIKMYLKEI GKIPLLTPAQ ERELARRAQM
160 170 180 190 200
GDKKAKEKLI TSNLRLVVSI AKRYMGRGLS FQDLIQEGNI GLLKAVEKFD
210 220 230 240 250
WRKGYKFSTY ATWWIRQAIT RAIADQARTI RIPVHMVETI NKLNRLRREY
260 270 280 290 300
YQKHGEEPSI EELAKMMGKP PEKIKEILEA AKETISLESP IGEDEDSSIE
310 320 330 340 350
DFVADDSIAS PKKEAMRMLM REELEKVLKT LSPREAMVLR MRYGLLDGKP
360 370 380 390
KTLEEVGQYF NVTRERIRQI EVKALRKLRH PSRSKYLKSL LSLMDENEG
Length:399
Mass (Da):46,534
Last modified:May 30, 2000 - v3
Checksum:iBF9B519E8C4890A7
GO

Sequence cautioni

The sequence AAC44889 differs from that shown. Reason: Erroneous initiation.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U67423 Genomic DNA Translation: AAC44889.2 Different initiation.
AE000512 Genomic DNA Translation: AAD36519.1
PIRiG72253
RefSeqiNP_229250.1, NC_000853.1
WP_010865345.1, NZ_CP011107.1

Genome annotation databases

EnsemblBacteriaiAAD36519; AAD36519; TM_1451
GeneIDi898025
KEGGitma:TM1451
tmi:THEMA_07060
PATRICifig|243274.18.peg.1363

Similar proteinsi

Entry informationi

Entry nameiSIGA_THEMA
AccessioniPrimary (citable) accession number: P77994
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: May 23, 2018
This is version 139 of the entry and version 3 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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