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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: Annotation score: 3 out of 5-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

Complete GO annotation...

Keywords - Molecular functioni

Sigma factor

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

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

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

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

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.
OMAiIDEVYEQ.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00963. Sigma70_RpoD_SigA. 1 hit.
InterProiIPR014284. 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.
IPR012760. RNA_pol_sigma_RpoD_C.
IPR028630. Sigma70_RpoD.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF03979. 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.
[Graphical view]
PRINTSiPR00046. SIGMA70FCT.
SUPFAMiSSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]

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. NC_000853.1.

Genome annotation databases

EnsemblBacteriaiAAD36519; AAD36519; TM_1451.
GeneIDi898025.
KEGGitma:TM1451.
tmi:THEMA_07060.
PATRICi23937854. VBITheMar51294_1465.

Cross-referencesi

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. NC_000853.1.

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...

Protein-protein interaction databases

STRINGi243274.TM1451.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAD36519; AAD36519; TM_1451.
GeneIDi898025.
KEGGitma:TM1451.
tmi:THEMA_07060.
PATRICi23937854. VBITheMar51294_1465.

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
InParanoidiP77994.
KOiK03086.
OMAiIDEVYEQ.

Miscellaneous databases

EvolutionaryTraceiP77994.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00963. Sigma70_RpoD_SigA. 1 hit.
InterProiIPR014284. 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.
IPR012760. RNA_pol_sigma_RpoD_C.
IPR028630. Sigma70_RpoD.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamiPF03979. 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.
[Graphical view]
PRINTSiPR00046. SIGMA70FCT.
SUPFAMiSSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsiTIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSIGA_THEMA
AccessioniPrimary (citable) accession number: P77994
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: May 30, 2000
Last modified: November 2, 2016
This is version 129 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.