SIGA_MYCTU
ID SIGA_MYCTU Reviewed; 528 AA.
AC P9WGI1; L0TAM5; O08495; O08513; P0A602; Q60162;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 51.
DE RecName: Full=RNA polymerase sigma factor SigA {ECO:0000255|HAMAP-Rule:MF_00963};
DE Short=Sigma-A;
GN Name=sigA {ECO:0000255|HAMAP-Rule:MF_00963}; Synonyms=mysA, rpoD, rpoV;
GN OrderedLocusNames=Rv2703; ORFNames=MTCY05A6.24;
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 [GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=7489918; DOI=10.1016/0378-1119(95)00427-8;
RA Doukhan L., Predich M., Nair G., Dussurget O., Mandic-Mulec I., Cole S.T.,
RA Smith D.R., Smith I.;
RT "Genomic organization of the mycobacterial sigma gene cluster.";
RL Gene 165:67-70(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 35801 / TMC 107 / Erdman;
RX PubMed=7644534; DOI=10.1073/pnas.92.17.8036;
RA Collins D.M., Kawakami R.P., de Lisle G.W., Pascopella L., Bloom B.R.,
RA Jacobs W.R.;
RT "Mutation of the principal sigma factor causes loss of virulence in a
RT strain of the Mycobacterium tuberculosis complex.";
RL Proc. Natl. Acad. Sci. U.S.A. 92:8036-8040(1995).
RN [3]
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 [4]
RP SUBUNIT, INDUCTION, AND HALF-LIFE.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9882660; DOI=10.1128/jb.181.2.469-476.1999;
RA Hu Y., Coates A.R.;
RT "Transcription of two sigma 70 homologue genes, sigA and sigB, in
RT stationary-phase Mycobacterium tuberculosis.";
RL J. Bacteriol. 181:469-476(1999).
RN [5]
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 [6]
RP INDUCTION FOLLOWING STARVATION.
RC STRAIN=ATCC 25618 / H37Rv / NCTC 7416;
RX PubMed=11929527; DOI=10.1046/j.1365-2958.2002.02779.x;
RA Betts J.C., Lukey P.T., Robb L.C., McAdam R.A., Duncan K.;
RT "Evaluation of a nutrient starvation model of Mycobacterium tuberculosis
RT persistence by gene and protein expression profiling.";
RL Mol. Microbiol. 43:717-731(2002).
RN [7]
RP FUNCTION AS A SIGMA FACTOR.
RX PubMed=12354223; DOI=10.1046/j.1365-2958.2002.03135.x;
RA Beaucher J., Rodrigue S., Jacques P.E., Smith I., Brzezinski R.,
RA Gaudreau L.;
RT "Novel Mycobacterium tuberculosis anti-sigma factor antagonists control
RT sigmaF activity by distinct mechanisms.";
RL Mol. Microbiol. 45:1527-1540(2002).
RN [8]
RP INTERACTION WITH WHIB3, AND MUTAGENESIS OF ARG-515.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=11880648; DOI=10.1073/pnas.052705399;
RA Steyn A.J., Collins D.M., Hondalus M.K., Jacobs W.R. Jr., Kawakami R.P.,
RA Bloom B.R.;
RT "Mycobacterium tuberculosis WhiB3 interacts with RpoV to affect host
RT survival but is dispensable for in vivo growth.";
RL Proc. Natl. Acad. Sci. U.S.A. 99:3147-3152(2002).
RN [9]
RP IDENTIFICATION AS A DRUG TARGET [LARGE SCALE ANALYSIS].
RX PubMed=19099550; DOI=10.1186/1752-0509-2-109;
RA Raman K., Yeturu K., Chandra N.;
RT "targetTB: a target identification pipeline for Mycobacterium tuberculosis
RT through an interactome, reactome and genome-scale structural analysis.";
RL BMC Syst. Biol. 2:109-109(2008).
RN [10]
RP FUNCTION AS A SIGMA FACTOR.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=20729364; DOI=10.1128/jb.00687-10;
RA Hartkoorn R.C., Sala C., Magnet S.J., Chen J.M., Pojer F., Cole S.T.;
RT "Sigma factor F does not prevent rifampin inhibition of RNA polymerase or
RT cause rifampin tolerance in Mycobacterium tuberculosis.";
RL J. Bacteriol. 192:5472-5479(2010).
RN [11]
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 [12]
RP FUNCTION AS A SIGMA FACTOR, AND SUBUNIT.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=22570422; DOI=10.1093/nar/gks346;
RA Hu Y., Morichaud Z., Chen S., Leonetti J.P., Brodolin K.;
RT "Mycobacterium tuberculosis RbpA protein is a new type of transcriptional
RT activator that stabilizes the sigma A-containing RNA polymerase
RT holoenzyme.";
RL Nucleic Acids Res. 40:6547-6557(2012).
RN [13]
RP INTERACTION WITH RBPA.
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=23548911; DOI=10.1074/jbc.m113.459883;
RA Bortoluzzi A., Muskett F.W., Waters L.C., Addis P.W., Rieck B., Munder T.,
RA Schleier S., Forti F., Ghisotti D., Carr M.D., O'Hare H.M.;
RT "Mycobacterium tuberculosis RNA polymerase-binding protein A (RbpA) and its
RT interactions with sigma factors.";
RL J. Biol. Chem. 288:14438-14450(2013).
RN [14]
RP INTERACTION WITH RBPA, AND SUBUNIT.
RX PubMed=23605043; DOI=10.1093/nar/gkt277;
RA Tabib-Salazar A., Liu B., Doughty P., Lewis R.A., Ghosh S., Parsy M.L.,
RA Simpson P.J., O'Dwyer K., Matthews S.J., Paget M.S.;
RT "The actinobacterial transcription factor RbpA binds to the principal sigma
RT subunit of RNA polymerase.";
RL Nucleic Acids Res. 41:5679-5691(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. This sigma factor is the primary sigma factor during
CC exponential growth (Probable). {ECO:0000305|PubMed:12354223,
CC ECO:0000305|PubMed:20729364, ECO:0000305|PubMed:22570422}.
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 with WhiB3 and probably with RbpA probably via
CC its sigma-2 region. {ECO:0000255|HAMAP-Rule:MF_00963,
CC ECO:0000269|PubMed:11880648, ECO:0000269|PubMed:22570422,
CC ECO:0000269|PubMed:23548911, ECO:0000269|PubMed:23605043,
CC ECO:0000269|PubMed:9882660}.
CC -!- INTERACTION:
CC P9WGI1; P9WF41: whiB3; NbExp=3; IntAct=EBI-11859464, EBI-11859434;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00963}.
CC -!- INDUCTION: Constitutively expressed under all conditions tested except
CC for 3-fold reduction in stationary phase, standing culture and upon
CC growth in H(2)O. 2-fold induced by starvation. Half-life of over 40
CC minutes. {ECO:0000269|PubMed:10027986, ECO:0000269|PubMed:11929527,
CC ECO:0000269|PubMed:9882660}.
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 (By similarity). {ECO:0000250}.
CC -!- MISCELLANEOUS: Was identified as a high-confidence drug target.
CC {ECO:0000305|PubMed:19099550}.
CC -!- SIMILARITY: Belongs to the sigma-70 factor family. RpoD/SigA subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_00963}.
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DR EMBL; U10059; AAA86043.1; -; Genomic_DNA.
DR EMBL; U21134; AAA81644.1; -; Genomic_DNA.
DR EMBL; AL123456; CCP45501.1; -; Genomic_DNA.
DR PIR; B70531; B70531.
DR RefSeq; NP_217219.1; NC_000962.3.
DR RefSeq; WP_003413944.1; NZ_NVQJ01000017.1.
DR PDB; 4X8K; X-ray; 2.20 A; A=236-364.
DR PDB; 5UH5; X-ray; 3.75 A; F=1-528.
DR PDB; 5UH6; X-ray; 3.84 A; F=1-528.
DR PDB; 5UH8; X-ray; 4.18 A; F=1-528.
DR PDB; 5UH9; X-ray; 4.40 A; F=1-528.
DR PDB; 5UHA; X-ray; 3.91 A; F=1-528.
DR PDB; 5UHB; X-ray; 4.29 A; F=1-528.
DR PDB; 5UHC; X-ray; 3.80 A; F=1-528.
DR PDB; 5UHD; X-ray; 4.01 A; F=1-528.
DR PDB; 5UHE; X-ray; 4.04 A; F=1-528.
DR PDB; 5UHF; X-ray; 4.34 A; F=1-528.
DR PDB; 5UHG; X-ray; 3.97 A; F=1-528.
DR PDB; 6BZO; EM; 3.38 A; F=1-528.
DR PDB; 6C04; EM; 3.27 A; F=1-528.
DR PDB; 6C05; EM; 5.15 A; F=1-528.
DR PDB; 6C06; EM; 5.15 A; F=1-528.
DR PDB; 6EDT; EM; -; F=1-528.
DR PDB; 6EE8; EM; 3.92 A; F=1-528.
DR PDB; 6EEC; EM; 3.55 A; F=1-528.
DR PDB; 6FBV; EM; 3.50 A; F=1-528.
DR PDB; 6M7J; EM; 4.40 A; F=1-528.
DR PDB; 6ONO; X-ray; 1.85 A; B/D=417-528.
DR PDB; 6ONU; X-ray; 1.85 A; B/D/F/H=417-528.
DR PDB; 6VVX; EM; 3.39 A; F=1-528.
DR PDB; 6VVY; EM; 3.42 A; F=1-528.
DR PDB; 6VVZ; EM; 3.72 A; F=1-528.
DR PDB; 6VW0; EM; 3.59 A; F=1-528.
DR PDB; 7KIF; EM; 2.94 A; F=1-528.
DR PDB; 7KIM; EM; 3.38 A; F=1-528.
DR PDB; 7KIN; EM; 2.74 A; F=1-528.
DR PDB; 7KUF; X-ray; 2.60 A; B=446-528.
DR PDB; 7KUG; X-ray; 1.55 A; B/D=446-528.
DR PDBsum; 4X8K; -.
DR PDBsum; 5UH5; -.
DR PDBsum; 5UH6; -.
DR PDBsum; 5UH8; -.
DR PDBsum; 5UH9; -.
DR PDBsum; 5UHA; -.
DR PDBsum; 5UHB; -.
DR PDBsum; 5UHC; -.
DR PDBsum; 5UHD; -.
DR PDBsum; 5UHE; -.
DR PDBsum; 5UHF; -.
DR PDBsum; 5UHG; -.
DR PDBsum; 6BZO; -.
DR PDBsum; 6C04; -.
DR PDBsum; 6C05; -.
DR PDBsum; 6C06; -.
DR PDBsum; 6EDT; -.
DR PDBsum; 6EE8; -.
DR PDBsum; 6EEC; -.
DR PDBsum; 6FBV; -.
DR PDBsum; 6M7J; -.
DR PDBsum; 6ONO; -.
DR PDBsum; 6ONU; -.
DR PDBsum; 6VVX; -.
DR PDBsum; 6VVY; -.
DR PDBsum; 6VVZ; -.
DR PDBsum; 6VW0; -.
DR PDBsum; 7KIF; -.
DR PDBsum; 7KIM; -.
DR PDBsum; 7KIN; -.
DR PDBsum; 7KUF; -.
DR PDBsum; 7KUG; -.
DR AlphaFoldDB; P9WGI1; -.
DR SMR; P9WGI1; -.
DR IntAct; P9WGI1; 3.
DR STRING; 83332.Rv2703; -.
DR PaxDb; P9WGI1; -.
DR GeneID; 45426691; -.
DR GeneID; 887477; -.
DR KEGG; mtu:Rv2703; -.
DR TubercuList; Rv2703; -.
DR eggNOG; COG0568; Bacteria.
DR OMA; MAWICRD; -.
DR PhylomeDB; P9WGI1; -.
DR BRENDA; 2.7.7.6; 3445.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0009274; C:peptidoglycan-based cell wall; HDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0003677; F:DNA binding; IDA:MTBBASE.
DR GO; GO:0016987; F:sigma factor activity; IDA:MTBBASE.
DR GO; GO:0006352; P:DNA-templated transcription, initiation; IEA:UniProtKB-UniRule.
DR GO; GO:0009415; P:response to water; IEP:MTBBASE.
DR DisProt; DP02525; -.
DR Gene3D; 1.10.10.10; -; 2.
DR HAMAP; MF_00963; Sigma70_RpoD_SigA; 1.
DR InterPro; IPR014284; RNA_pol_sigma-70_dom.
DR InterPro; IPR000943; RNA_pol_sigma70.
DR InterPro; IPR009042; RNA_pol_sigma70_r1_2.
DR InterPro; IPR007627; RNA_pol_sigma70_r2.
DR InterPro; IPR007624; RNA_pol_sigma70_r3.
DR InterPro; IPR007630; RNA_pol_sigma70_r4.
DR InterPro; IPR013325; RNA_pol_sigma_r2.
DR InterPro; IPR013324; RNA_pol_sigma_r3/r4-like.
DR InterPro; IPR012760; RNA_pol_sigma_RpoD_C.
DR InterPro; IPR028630; Sigma70_RpoD.
DR InterPro; IPR036388; WH-like_DNA-bd_sf.
DR Pfam; PF00140; Sigma70_r1_2; 1.
DR Pfam; PF04542; Sigma70_r2; 1.
DR Pfam; PF04539; Sigma70_r3; 1.
DR Pfam; PF04545; Sigma70_r4; 1.
DR PRINTS; PR00046; SIGMA70FCT.
DR SUPFAM; SSF88659; SSF88659; 2.
DR SUPFAM; SSF88946; SSF88946; 1.
DR TIGRFAMs; TIGR02393; RpoD_Cterm; 1.
DR TIGRFAMs; TIGR02937; sigma70-ECF; 1.
DR PROSITE; PS00715; SIGMA70_1; 1.
DR PROSITE; PS00716; SIGMA70_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; DNA-binding; Reference proteome; Sigma factor;
KW Transcription; Transcription regulation.
FT CHAIN 1..528
FT /note="RNA polymerase sigma factor SigA"
FT /id="PRO_0000093901"
FT DNA_BIND 489..508
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 1..211
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 225..259
FT /note="Sigma-70 factor domain-1"
FT REGION 295..365
FT /note="Sigma-70 factor domain-2"
FT REGION 374..450
FT /note="Sigma-70 factor domain-3"
FT REGION 463..516
FT /note="Sigma-70 factor domain-4"
FT MOTIF 319..322
FT /note="Interaction with polymerase core subunit RpoC"
FT COMPBIAS 1..26
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 61..76
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 96..113
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 114..172
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 192..211
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MUTAGEN 515
FT /note="R->H: Loss of interaction with WhiB3."
FT /evidence="ECO:0000269|PubMed:11880648"
FT TURN 207..209
FT /evidence="ECO:0007829|PDB:7KIF"
FT HELIX 212..220
FT /evidence="ECO:0007829|PDB:7KIN"
FT HELIX 227..235
FT /evidence="ECO:0007829|PDB:7KIN"
FT HELIX 243..267
FT /evidence="ECO:0007829|PDB:4X8K"
FT TURN 268..270
FT /evidence="ECO:0007829|PDB:4X8K"
FT HELIX 275..297
FT /evidence="ECO:0007829|PDB:4X8K"
FT HELIX 300..308
FT /evidence="ECO:0007829|PDB:4X8K"
FT STRAND 312..315
FT /evidence="ECO:0007829|PDB:4X8K"
FT HELIX 317..334
FT /evidence="ECO:0007829|PDB:4X8K"
FT HELIX 337..339
FT /evidence="ECO:0007829|PDB:7KIN"
FT HELIX 343..362
FT /evidence="ECO:0007829|PDB:4X8K"
FT STRAND 363..366
FT /evidence="ECO:0007829|PDB:7KIN"
FT HELIX 370..390
FT /evidence="ECO:0007829|PDB:7KIN"
FT HELIX 396..402
FT /evidence="ECO:0007829|PDB:7KIN"
FT HELIX 409..416
FT /evidence="ECO:0007829|PDB:7KIN"
FT STRAND 421..423
FT /evidence="ECO:0007829|PDB:6BZO"
FT STRAND 428..431
FT /evidence="ECO:0007829|PDB:7KIN"
FT HELIX 435..437
FT /evidence="ECO:0007829|PDB:7KIF"
FT STRAND 438..441
FT /evidence="ECO:0007829|PDB:7KIN"
FT TURN 447..449
FT /evidence="ECO:0007829|PDB:6C04"
FT HELIX 453..464
FT /evidence="ECO:0007829|PDB:7KUG"
FT HELIX 469..479
FT /evidence="ECO:0007829|PDB:7KUG"
FT TURN 480..483
FT /evidence="ECO:0007829|PDB:7KUG"
FT HELIX 489..496
FT /evidence="ECO:0007829|PDB:7KUG"
FT HELIX 500..515
FT /evidence="ECO:0007829|PDB:7KUG"
FT HELIX 517..520
FT /evidence="ECO:0007829|PDB:7KUG"
FT HELIX 521..523
FT /evidence="ECO:0007829|PDB:7KUG"
FT HELIX 524..526
FT /evidence="ECO:0007829|PDB:7KIN"
SQ SEQUENCE 528 AA; 57800 MW; 2252FD53419EA8B8 CRC64;
MAATKASTAT DEPVKRTATK SPAASASGAK TGAKRTAAKS ASGSPPAKRA TKPAARSVKP
ASAPQDTTTS TIPKRKTRAA AKSAAAKAPS ARGHATKPRA PKDAQHEAAT DPEDALDSVE
ELDAEPDLDV EPGEDLDLDA ADLNLDDLED DVAPDADDDL DSGDDEDHED LEAEAAVAPG
QTADDDEEIA EPTEKDKASG DFVWDEDESE ALRQARKDAE LTASADSVRA YLKQIGKVAL
LNAEEEVELA KRIEAGLYAT QLMTELSERG EKLPAAQRRD MMWICRDGDR AKNHLLEANL
RLVVSLAKRY TGRGMAFLDL IQEGNLGLIR AVEKFDYTKG YKFSTYATWW IRQAITRAMA
DQARTIRIPV HMVEVINKLG RIQRELLQDL GREPTPEELA KEMDITPEKV LEIQQYAREP
ISLDQTIGDE GDSQLGDFIE DSEAVVAVDA VSFTLLQDQL QSVLDTLSER EAGVVRLRFG
LTDGQPRTLD EIGQVYGVTR ERIRQIESKT MSKLRHPSRS QVLRDYLD
