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ECF RNA polymerase sigma factor SigD (ECF sigma factor SigD) (Alternative RNA polymerase sigma factor SigD) (RNA polymerase sigma-D factor) (Sigma-D factor)

 RPSD_MYCTU              Reviewed;         212 AA.
P9WGG9; L0TFB3; P66811; Q50712;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
25-APR-2018, entry version 25.
RecName: Full=ECF RNA polymerase sigma factor SigD;
Short=ECF sigma factor SigD;
AltName: Full=Alternative RNA polymerase sigma factor SigD;
AltName: Full=RNA polymerase sigma-D factor;
AltName: Full=Sigma-D factor;
Name=sigD; OrderedLocusNames=Rv3414c; ORFNames=MTCY78.15;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
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., 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.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
INDUCTION.
STRAIN=ATCC 25618 / H37Rv;
PubMed=10027986; DOI=10.1046/j.1365-2958.1999.01212.x;
Manganelli R., Dubnau E., Tyagi S., Kramer F.R., Smith I.;
"Differential expression of 10 sigma factor genes in Mycobacterium
tuberculosis.";
Mol. Microbiol. 31:715-724(1999).
[3]
FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
STRAIN=ATCC 25618 / H37Rv;
PubMed=15375142; DOI=10.1128/JB.186.19.6605-6616.2004;
Raman S., Hazra R., Dascher C.C., Husson R.N.;
"Transcription regulation by the Mycobacterium tuberculosis
alternative sigma factor SigD and its role in virulence.";
J. Bacteriol. 186:6605-6616(2004).
[4]
INTERACTION WITH ANTI-SIGMA FACTOR RSDA.
PubMed=20600947; DOI=10.1016/j.pep.2010.06.018;
Thakur K.G., Jaiswal R.K., Shukla J.K., Praveena T., Gopal B.;
"Over-expression and purification strategies for recombinant multi-
protein oligomers: a case study of Mycobacterium tuberculosis
sigma/anti-sigma factor protein complexes.";
Protein Expr. Purif. 74:223-230(2010).
[5]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[6]
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 141-212 IN COMPLEX WITH RSDA,
AND SUBUNIT.
STRAIN=ATCC 25618 / H37Rv;
PubMed=23314154; DOI=10.1093/nar/gks1468;
Jaiswal R.K., Prabha T.S., Manjeera G., Gopal B.;
"Mycobacterium tuberculosis RsdA provides a conformational rationale
for selective regulation of sigma-factor activity by proteolysis.";
Nucleic Acids Res. 41:3414-3423(2013).
-!- 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.
{ECO:0000269|PubMed:15375142}.
-!- SUBUNIT: 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. {ECO:0000269|PubMed:20600947,
ECO:0000269|PubMed:23314154}.
-!- INDUCTION: Positively autoregulates, probably directly, expressed
at a relatively high level throughout exponential growth and
during stationary phase. Expression decreases during O(2)
depletion (hypoxia) (PubMed:15375142) and after heat shock (5-
fold, 45 degrees Celsius) (PubMed:10027986).
{ECO:0000269|PubMed:10027986, ECO:0000269|PubMed:15375142}.
-!- 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). {ECO:0000250}.
-!- DOMAIN: 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).
{ECO:0000250}.
-!- 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.
{ECO:0000269|PubMed:15375142}.
-!- 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). {ECO:0000305}.
-!- SIMILARITY: Belongs to the sigma-70 factor family. ECF subfamily.
{ECO:0000305}.
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EMBL; AL123456; CCP46236.1; -; Genomic_DNA.
PIR; C70737; C70737.
RefSeq; NP_217931.1; NC_000962.3.
RefSeq; WP_003418013.1; NZ_KK339370.1.
PDB; 3VEP; X-ray; 2.50 A; A/D/E/H=141-212.
PDB; 3VFZ; X-ray; 1.90 A; A/B=141-212.
PDBsum; 3VEP; -.
PDBsum; 3VFZ; -.
ProteinModelPortal; P9WGG9; -.
SMR; P9WGG9; -.
STRING; 83332.Rv3414c; -.
PaxDb; P9WGG9; -.
EnsemblBacteria; CCP46236; CCP46236; Rv3414c.
GeneID; 887594; -.
KEGG; mtu:Rv3414c; -.
KEGG; mtv:RVBD_3414c; -.
PATRIC; fig|83332.111.peg.3804; -.
TubercuList; Rv3414c; -.
eggNOG; ENOG4105UYU; Bacteria.
eggNOG; ENOG4111TYT; LUCA.
KO; K03088; -.
OMA; AVKVGIH; -.
PhylomeDB; P9WGG9; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0016987; F:bacterial sigma factor activity; IMP:MTBBASE.
GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
GO; GO:0003700; F:DNA binding transcription factor activity; IEA:InterPro.
GO; GO:0006352; P:DNA-templated transcription, initiation; IEA:InterPro.
GO; GO:0009405; P:pathogenesis; IMP:MTBBASE.
GO; GO:0019217; P:regulation of fatty acid metabolic process; IDA:MTBBASE.
GO; GO:0050708; P:regulation of protein secretion; IDA:MTBBASE.
GO; GO:0009408; P:response to heat; IEP:MTBBASE.
Gene3D; 1.10.10.10; -; 1.
InterPro; IPR014284; RNA_pol_sigma-70_dom.
InterPro; IPR000838; RNA_pol_sigma70_ECF_CS.
InterPro; IPR007627; RNA_pol_sigma70_r2.
InterPro; IPR013249; RNA_pol_sigma70_r4_t2.
InterPro; IPR013325; RNA_pol_sigma_r2.
InterPro; IPR013324; RNA_pol_sigma_r3/r4-like.
InterPro; IPR036388; WH-like_DNA-bd_sf.
Pfam; PF04542; Sigma70_r2; 1.
Pfam; PF08281; Sigma70_r4_2; 1.
SUPFAM; SSF88659; SSF88659; 1.
SUPFAM; SSF88946; SSF88946; 1.
TIGRFAMs; TIGR02937; sigma70-ECF; 1.
PROSITE; PS01063; SIGMA70_ECF; 1.
1: Evidence at protein level;
3D-structure; Complete proteome; DNA-binding; Reference proteome;
Sigma factor; Transcription; Transcription regulation; Virulence.
CHAIN 1 212 ECF RNA polymerase sigma factor SigD.
/FTId=PRO_0000094023.
DNA_BIND 176 195 H-T-H motif. {ECO:0000250}.
REGION 49 119 Sigma-70 factor domain-2.
REGION 152 201 Sigma-70 factor domain-4.
MOTIF 75 78 Polymerase core binding. {ECO:0000255}.
HELIX 147 155 {ECO:0000244|PDB:3VFZ}.
HELIX 160 170 {ECO:0000244|PDB:3VFZ}.
HELIX 176 183 {ECO:0000244|PDB:3VFZ}.
HELIX 187 206 {ECO:0000244|PDB:3VFZ}.
SEQUENCE 212 AA; 22919 MW; 12A157F6F66BB0C3 CRC64;
MVDPGVSPGC VRFVTLEISP SMTMQGERLD AVVAEAVAGD RNALREVLET IRPIVVRYCR
ARVGTVERSG LSADDVAQEV CLATITALPR YRDRGRPFLA FLYGIAAHKV ADAHRAAGRD
RAYPAETLPE RWSADAGPEQ MAIEADSVTR MNELLEILPA KQREILILRV VVGLSAEETA
AAVGSTTGAV RVAQHRALQR LKDEIVAAGD YA


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