RPSD_MYCTU
ID RPSD_MYCTU Reviewed; 212 AA.
AC P9WGG9; L0TFB3; P66811; Q50712;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 25-MAY-2022, entry version 42.
DE RecName: Full=ECF RNA polymerase sigma factor SigD;
DE Short=ECF sigma factor SigD;
DE AltName: Full=Alternative RNA polymerase sigma factor SigD;
DE AltName: Full=RNA polymerase sigma-D factor;
DE AltName: Full=Sigma-D factor;
GN Name=sigD; OrderedLocusNames=Rv3414c; ORFNames=MTCY78.15;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP INDUCTION.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=10027986; DOI=10.1046/j.1365-2958.1999.01212.x;
RA Manganelli R., Dubnau E., Tyagi S., Kramer F.R., Smith I.;
RT "Differential expression of 10 sigma factor genes in Mycobacterium
RT tuberculosis.";
RL Mol. Microbiol. 31:715-724(1999).
RN [3]
RP FUNCTION, INDUCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=15375142; DOI=10.1128/jb.186.19.6605-6616.2004;
RA Raman S., Hazra R., Dascher C.C., Husson R.N.;
RT "Transcription regulation by the Mycobacterium tuberculosis alternative
RT sigma factor SigD and its role in virulence.";
RL J. Bacteriol. 186:6605-6616(2004).
RN [4]
RP INTERACTION WITH ANTI-SIGMA FACTOR RSDA.
RX PubMed=20600947; DOI=10.1016/j.pep.2010.06.018;
RA Thakur K.G., Jaiswal R.K., Shukla J.K., Praveena T., Gopal B.;
RT "Over-expression and purification strategies for recombinant multi-protein
RT oligomers: a case study of Mycobacterium tuberculosis sigma/anti-sigma
RT factor protein complexes.";
RL Protein Expr. Purif. 74:223-230(2010).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 141-212 IN COMPLEX WITH RSDA, AND
RP SUBUNIT.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=23314154; DOI=10.1093/nar/gks1468;
RA Jaiswal R.K., Prabha T.S., Manjeera G., Gopal B.;
RT "Mycobacterium tuberculosis RsdA provides a conformational rationale for
RT selective regulation of sigma-factor activity by proteolysis.";
RL Nucleic Acids Res. 41:3414-3423(2013).
CC -!- FUNCTION: Sigma factors are initiation factors that promote the
CC attachment of RNA polymerase to specific initiation sites and are then
CC released. Extracytoplasmic function (ECF) sigma factors are held in an
CC inactive form by an anti-sigma factor until released by regulated
CC intramembrane proteolysis. {ECO:0000269|PubMed:15375142}.
CC -!- SUBUNIT: Interacts transiently with the RNA polymerase catalytic core
CC formed by RpoA, RpoB, RpoC and RpoZ (2 alpha, 1 beta, 1 beta' and 1
CC omega subunit) to form the RNA polymerase holoenzyme that can initiate
CC transcription. Interacts (via sigma-70 factor domain 4) with RsdA.
CC {ECO:0000269|PubMed:20600947, ECO:0000269|PubMed:23314154}.
CC -!- INDUCTION: Positively autoregulates, probably directly, expressed at a
CC relatively high level throughout exponential growth and during
CC stationary phase. Expression decreases during O(2) depletion (hypoxia)
CC (PubMed:15375142) and after heat shock (5-fold, 45 degrees Celsius)
CC (PubMed:10027986). {ECO:0000269|PubMed:10027986,
CC ECO:0000269|PubMed:15375142}.
CC -!- DOMAIN: The sigma-70 factor domain-2 mediates sequence-specific
CC interaction with the -10 element in promoter DNA, and plays an
CC important role in melting the double-stranded DNA and the formation of
CC the transcription bubble. The sigma-70 factor domain-2 mediates
CC interaction with the RNA polymerase subunits RpoB and RpoC (By
CC similarity). {ECO:0000250}.
CC -!- DOMAIN: The sigma-70 factor domain-4 contains a helix-turn-helix (H-T-
CC H) motif that mediates interaction with the -35 element in promoter
CC DNA. The domain also mediates interaction with the RNA polymerase
CC subunit RpoA. Interactions between sigma-70 factor domain-4 and anti-
CC sigma factors prevents interaction of sigma factors with the RNA
CC polymerase catalytic core (By similarity). {ECO:0000250}.
CC -!- DISRUPTION PHENOTYPE: Not essential for growth in culture. Upon
CC disruption about 260 genes show significantly decreased expression
CC while about 200 showed increased expression. BALB/c mice infected with
CC the disruption mutant showed a moderate but significant decrease in
CC virulence, surviving about 30% longer than wild-type.
CC {ECO:0000269|PubMed:15375142}.
CC -!- MISCELLANEOUS: Extracytoplasmic function sigma factors (ECF) are held
CC in an inactive form by an anti-sigma factor until released by regulated
CC intramembrane proteolysis (RIP). RIP occurs when an extracytoplasmic
CC signal triggers a concerted proteolytic cascade to transmit information
CC and elicit cellular responses. The membrane-spanning anti-sigma factor
CC is first cut extracytoplasmically (site-1 protease, S1P), then within
CC the membrane itself (site-2 protease, S2P), while cytoplasmic proteases
CC finish degrading the regulatory protein, liberating SigD (Probable).
CC {ECO:0000305}.
CC -!- SIMILARITY: Belongs to the sigma-70 factor family. ECF subfamily.
CC {ECO:0000305}.
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DR EMBL; AL123456; CCP46236.1; -; Genomic_DNA.
DR PIR; C70737; C70737.
DR RefSeq; NP_217931.1; NC_000962.3.
DR RefSeq; WP_003418013.1; NZ_KK339370.1.
DR PDB; 3VEP; X-ray; 2.50 A; A/D/E/H=141-212.
DR PDB; 3VFZ; X-ray; 1.90 A; A/B=141-212.
DR PDBsum; 3VEP; -.
DR PDBsum; 3VFZ; -.
DR AlphaFoldDB; P9WGG9; -.
DR SMR; P9WGG9; -.
DR STRING; 83332.Rv3414c; -.
DR PaxDb; P9WGG9; -.
DR DNASU; 887594; -.
DR GeneID; 45427410; -.
DR GeneID; 887594; -.
DR KEGG; mtu:Rv3414c; -.
DR PATRIC; fig|83332.111.peg.3804; -.
DR TubercuList; Rv3414c; -.
DR eggNOG; COG1595; Bacteria.
DR OMA; AVKVGIH; -.
DR PhylomeDB; P9WGG9; -.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016987; F:sigma factor activity; IMP:MTBBASE.
DR GO; GO:0006352; P:DNA-templated transcription, initiation; IEA:InterPro.
DR GO; GO:0009408; P:response to heat; IEP:MTBBASE.
DR Gene3D; 1.10.10.10; -; 1.
DR InterPro; IPR039425; RNA_pol_sigma-70-like.
DR InterPro; IPR014284; RNA_pol_sigma-70_dom.
DR InterPro; IPR000838; RNA_pol_sigma70_ECF_CS.
DR InterPro; IPR007627; RNA_pol_sigma70_r2.
DR InterPro; IPR013249; RNA_pol_sigma70_r4_t2.
DR InterPro; IPR013325; RNA_pol_sigma_r2.
DR InterPro; IPR013324; RNA_pol_sigma_r3/r4-like.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR PANTHER; PTHR43133; PTHR43133; 1.
DR Pfam; PF04542; Sigma70_r2; 1.
DR Pfam; PF08281; Sigma70_r4_2; 1.
DR SUPFAM; SSF88659; SSF88659; 1.
DR SUPFAM; SSF88946; SSF88946; 1.
DR TIGRFAMs; TIGR02937; sigma70-ECF; 1.
DR PROSITE; PS01063; SIGMA70_ECF; 1.
PE 1: Evidence at protein level;
KW 3D-structure; DNA-binding; Reference proteome; Sigma factor; Transcription;
KW Transcription regulation; Virulence.
FT CHAIN 1..212
FT /note="ECF RNA polymerase sigma factor SigD"
FT /id="PRO_0000094023"
FT DNA_BIND 176..195
FT /note="H-T-H motif"
FT /evidence="ECO:0000250"
FT REGION 49..119
FT /note="Sigma-70 factor domain-2"
FT REGION 152..201
FT /note="Sigma-70 factor domain-4"
FT MOTIF 75..78
FT /note="Polymerase core binding"
FT /evidence="ECO:0000255"
FT HELIX 147..155
FT /evidence="ECO:0007829|PDB:3VFZ"
FT HELIX 160..170
FT /evidence="ECO:0007829|PDB:3VFZ"
FT HELIX 176..183
FT /evidence="ECO:0007829|PDB:3VFZ"
FT HELIX 187..206
FT /evidence="ECO:0007829|PDB:3VFZ"
SQ 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
