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P66811 (RPSD_MYCTU) Reviewed, UniProtKB/Swiss-Prot

Last modified March 19, 2014. Version 66. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
ECF RNA polymerase sigma factor SigD

Short name=ECF sigma factor SigD
Alternative name(s):
Alternative RNA polymerase sigma factor SigD
RNA polymerase sigma-D factor
Sigma-D factor
Gene names
Name:sigD
Ordered Locus Names:Rv3414c, MT3523
ORF Names:MTCY78.15
OrganismMycobacterium tuberculosis [Reference proteome] [HAMAP]
Taxonomic identifier1773 [NCBI]
Taxonomic lineageBacteriaActinobacteriaActinobacteridaeActinomycetalesCorynebacterineaeMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex

Protein attributes

Sequence length212 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. Extracytoplasmic function (ECF) sigma factors are held in an inactive form by an anti-sigma factor until released by regulated intramembrane proteolysis. Ref.4

Subunit structure

Interacts transiently with the RNA polymerase catalytic core formed by RpoA, RpoB, RpoC and RpoZ (2 alpha, 1 beta, 1 beta' and 1 omega subunit) to form the RNA polymerase holoenzyme that can initiate transcription. Interacts (via sigma-70 factor domain 4) with RsdA. Ref.5 Ref.6

Induction

Positively autoregulates, probably directly, expressed at a relatively high level throughout exponential growth and during stationary phase. Expression decreases during O2 depletion (hypoxia) (Ref.4) and after heat shock (5-fold, 45 degrees Celsius) (Ref.3). Ref.3 Ref.4

Domain

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.

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.

Disruption phenotype

Not essential for growth in culture. Upon disruption about 260 genes show significantly decreased expression while about 200 showed increased expression. BALB/c mice infected with the disruption mutant showed a moderate but significant decrease in virulence, surviving about 30% longer than wild-type. Ref.4

Miscellaneous

Extracytoplasmic function sigma factors (ECF) are held in an inactive form by an anti-sigma factor until released by regulated intramembrane proteolysis (RIP). RIP occurs when an extracytoplasmic signal triggers a concerted proteolytic cascade to transmit information and elicit cellular responses. The membrane-spanning anti-sigma factor is first cut extracytoplasmically (site-1 protease, S1P), then within the membrane itself (site-2 protease, S2P), while cytoplasmic proteases finish degrading the regulatory protein, liberating SigD Probable.

Sequence similarities

Belongs to the sigma-70 factor family. ECF subfamily.

Sequence caution

The sequence AAK47861.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 212212ECF RNA polymerase sigma factor SigD
PRO_0000094023

Regions

DNA binding176 – 19520H-T-H motif By similarity
Region49 – 11971Sigma-70 factor domain-2
Region152 – 20150Sigma-70 factor domain-4
Motif75 – 784Polymerase core binding Potential

Secondary structure

......... 212
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P66811 [UniParc].

Last modified October 11, 2004. Version 1.
Checksum: 12A157F6F66BB0C3

FASTA21222,919
        10         20         30         40         50         60 
MVDPGVSPGC VRFVTLEISP SMTMQGERLD AVVAEAVAGD RNALREVLET IRPIVVRYCR 

        70         80         90        100        110        120 
ARVGTVERSG LSADDVAQEV CLATITALPR YRDRGRPFLA FLYGIAAHKV ADAHRAAGRD 

       130        140        150        160        170        180 
RAYPAETLPE RWSADAGPEQ MAIEADSVTR MNELLEILPA KQREILILRV VVGLSAEETA 

       190        200        210 
AAVGSTTGAV RVAQHRALQR LKDEIVAAGD YA 

« Hide

References

« Hide 'large scale' references
[1]"Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence."
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K. expand/collapse author list , Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S., Barrell B.G.
Nature 393:537-544(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 25618 / H37Rv.
[2]"Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains."
Fleischmann R.D., Alland D., Eisen J.A., Carpenter L., White O., Peterson J.D., DeBoy R.T., Dodson R.J., Gwinn M.L., Haft D.H., Hickey E.K., Kolonay J.F., Nelson W.C., Umayam L.A., Ermolaeva M.D., Salzberg S.L., Delcher A., Utterback T.R. expand/collapse author list , Weidman J.F., Khouri H.M., Gill J., Mikula A., Bishai W., Jacobs W.R. Jr., Venter J.C., Fraser C.M.
J. Bacteriol. 184:5479-5490(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: CDC 1551 / Oshkosh.
[3]"Differential expression of 10 sigma factor genes in Mycobacterium tuberculosis."
Manganelli R., Dubnau E., Tyagi S., Kramer F.R., Smith I.
Mol. Microbiol. 31:715-724(1999) [PubMed] [Europe PMC] [Abstract]
Cited for: INDUCTION.
Strain: ATCC 25618 / H37Rv.
[4]"Transcription regulation by the Mycobacterium tuberculosis alternative sigma factor SigD and its role in virulence."
Raman S., Hazra R., Dascher C.C., Husson R.N.
J. Bacteriol. 186:6605-6616(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INDUCTION, DISRUPTION PHENOTYPE.
Strain: ATCC 25618 / H37Rv.
[5]"Over-expression and purification strategies for recombinant multi-protein oligomers: a case study of Mycobacterium tuberculosis sigma/anti-sigma factor protein complexes."
Thakur K.G., Jaiswal R.K., Shukla J.K., Praveena T., Gopal B.
Protein Expr. Purif. 74:223-230(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH ANTI-SIGMA FACTOR RSDA.
[6]"Mycobacterium tuberculosis RsdA provides a conformational rationale for selective regulation of sigma-factor activity by proteolysis."
Jaiswal R.K., Prabha T.S., Manjeera G., Gopal B.
Nucleic Acids Res. 41:3414-3423(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 141-212 IN COMPLEX WITH RSDA, SUBUNIT.
Strain: ATCC 25618 / H37Rv.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AE000516 Genomic DNA. Translation: AAK47861.1. Different initiation.
AL123456 Genomic DNA. Translation: CCP46236.1.
PIRC70737.
RefSeqNP_217931.1. NC_000962.3.
NP_338047.1. NC_002755.2.
YP_006516900.1. NC_018143.2.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3VEPX-ray2.50A/D/E/H141-212[»]
3VFZX-ray1.90A/B141-212[»]
ProteinModelPortalP66811.
SMRP66811. Positions 23-211.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING83332.Rv3414c.

Proteomic databases

PRIDEP66811.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAK47861; AAK47861; MT3523.
CCP46236; CCP46236; Rv3414c.
GeneID13317018.
887594.
923111.
KEGGmtc:MT3523.
mtu:Rv3414c.
mtv:RVBD_3414c.
PATRIC18129483. VBIMycTub22151_3837.

Organism-specific databases

TubercuListRv3414c.

Phylogenomic databases

eggNOGCOG1595.
HOGENOMHOG000094755.
KOK03088.
OMAMVVRYCR.
OrthoDBEOG69WFKH.
ProtClustDBPRK09648.

Enzyme and pathway databases

BioCycMTBRV:RV3414C-MONOMER.

Family and domain databases

Gene3D1.10.10.10. 1 hit.
InterProIPR014284. RNA_pol_sigma-70_dom.
IPR000838. RNA_pol_sigma70_ECF_CS.
IPR007627. RNA_pol_sigma70_r2.
IPR013249. RNA_pol_sigma70_r4_t2.
IPR013325. RNA_pol_sigma_r2.
IPR013324. RNA_pol_sigma_r3_r4.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view]
PfamPF04542. Sigma70_r2. 1 hit.
PF08281. Sigma70_r4_2. 1 hit.
[Graphical view]
SUPFAMSSF88659. SSF88659. 1 hit.
SSF88946. SSF88946. 1 hit.
TIGRFAMsTIGR02937. sigma70-ECF. 1 hit.
PROSITEPS01063. SIGMA70_ECF. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameRPSD_MYCTU
AccessionPrimary (citable) accession number: P66811
Secondary accession number(s): L0TFB3, Q50712
Entry history
Integrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: March 19, 2014
This is version 66 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh

Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names