SIGA_THEAQ
ID SIGA_THEAQ Reviewed; 438 AA.
AC Q9EZJ8;
DT 24-JUL-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 106.
DE RecName: Full=RNA polymerase sigma factor SigA {ECO:0000255|HAMAP-Rule:MF_00963};
GN Name=sigA {ECO:0000255|HAMAP-Rule:MF_00963};
OS Thermus aquaticus.
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=271;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND FUNCTION.
RX PubMed=11114902; DOI=10.1128/jb.183.1.71-76.2001;
RA Minakhin L., Nechaev S., Campbell E.A., Severinov K.;
RT "Recombinant Thermus aquaticus RNA polymerase, a new tool for structure-
RT based analysis of transcription.";
RL J. Bacteriol. 183:71-76(2001).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 366-438 IN COMPLEX WITH PROMOTER
RP DNA, PARTIAL PROTEIN SEQUENCE, FUNCTION, DOMAIN, DNA-BINDING, AND
RP IDENTIFICATION BY MASS SPECTROMETRY.
RX PubMed=11931761; DOI=10.1016/s1097-2765(02)00470-7;
RA Campbell E.A., Muzzin O., Chlenov M., Sun J.L., Olson C.A., Weinman O.,
RA Trester-Zedlitz M.L., Darst S.A.;
RT "Structure of the bacterial RNA polymerase promoter specificity sigma
RT subunit.";
RL Mol. Cell 9:527-539(2002).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (4.00 ANGSTROMS) OF 92-438 IN COMPLEX WITH RPOA;
RP RPOB; RPOC AND RPOZ, DOMAIN, DNA-BINDING, AND SUBUNIT.
RX PubMed=12016306; DOI=10.1126/science.1069594;
RA Murakami K.S., Masuda S., Darst S.A.;
RT "Structural basis of transcription initiation: RNA polymerase holoenzyme at
RT 4 A resolution.";
RL Science 296:1280-1284(2002).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (6.50 ANGSTROMS)IN COMPLEX WITH DNA; RPOA; RPOB; RPOC
RP AND RPOZ, DNA-BINDING, AND SUBUNIT.
RX PubMed=12016307; DOI=10.1126/science.1069595;
RA Murakami K.S., Masuda S., Campbell E.A., Muzzin O., Darst S.A.;
RT "Structural basis of transcription initiation: an RNA polymerase
RT holoenzyme-DNA complex.";
RL Science 296:1285-1290(2002).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 366-438 IN COMPLEX WITH PROMOTER
RP DNA, AND DNA-BINDING.
RX PubMed=14731393; DOI=10.1016/s1097-2765(03)00483-0;
RA Jain D., Nickels B.E., Sun L., Hochschild A., Darst S.A.;
RT "Structure of a ternary transcription activation complex.";
RL Mol. Cell 13:45-53(2004).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS) OF 92-332 IN COMPLEX WITH PROMOTER
RP DNA, DOMAIN, AND DNA-BINDING.
RX PubMed=22136875; DOI=10.1016/j.cell.2011.10.041;
RA Feklistov A., Darst S.A.;
RT "Structural basis for promoter-10 element recognition by the bacterial RNA
RT polymerase sigma subunit.";
RL Cell 147:1257-1269(2011).
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. {ECO:0000255|HAMAP-Rule:MF_00963,
CC ECO:0000269|PubMed:11114902, ECO:0000269|PubMed:11931761}.
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. {ECO:0000255|HAMAP-Rule:MF_00963,
CC ECO:0000269|PubMed:11931761, ECO:0000269|PubMed:12016306,
CC ECO:0000269|PubMed:12016307, ECO:0000269|PubMed:14731393,
CC ECO:0000269|PubMed:22136875}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00963}.
CC -!- DOMAIN: Contains 4 domains, connected by flexible linkers. In the
CC active conformation, the domains are in an extended conformation, each
CC making extensive interactions with the RNA polymerase catalytic core
CC (PubMed:11931761 and PubMed:12016306).
CC -!- DOMAIN: In the autoinhibited state, sigma-70 factor domain-1 packs
CC closely together with sigma-70 factor domains-2 and -4, contrary to the
CC extended conformation that is seen when the protein is part of the RNA
CC polymerase holoenzyme. {ECO:0000250}.
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
CC (PubMed:11931761 and PubMed:22136875).
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 (PubMed:11931761).
CC {ECO:0000269|PubMed:11931761}.
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; AF291720; AAG36964.1; -; Genomic_DNA.
DR PDB; 1KU2; X-ray; 2.90 A; A/B=92-332.
DR PDB; 1KU3; X-ray; 1.80 A; A=366-438.
DR PDB; 1KU7; X-ray; 2.40 A; A/D=366-438.
DR PDB; 1L9U; X-ray; 4.00 A; H/Q=92-438.
DR PDB; 1L9Z; X-ray; 6.50 A; H=1-438.
DR PDB; 1RIO; X-ray; 2.30 A; H=366-438.
DR PDB; 3LES; X-ray; 2.77 A; A/B=93-271.
DR PDB; 3LEV; X-ray; 2.50 A; A=93-271.
DR PDB; 3N97; X-ray; 3.25 A; A/D=366-438.
DR PDB; 3UGO; X-ray; 2.10 A; A=92-332.
DR PDB; 3UGP; X-ray; 2.70 A; A=92-332.
DR PDB; 4KI2; X-ray; 3.61 A; A/B=92-332.
DR PDB; 4XLN; X-ray; 4.00 A; F/L=92-438.
DR PDB; 4XLP; X-ray; 4.00 A; F/L=92-438.
DR PDB; 4XLQ; X-ray; 4.60 A; F/L=92-438.
DR PDB; 4XLR; X-ray; 4.30 A; F/L=92-438.
DR PDB; 4XLS; X-ray; 4.01 A; F/L=92-438.
DR PDB; 5TJG; X-ray; 2.60 A; F=92-438.
DR PDBsum; 1KU2; -.
DR PDBsum; 1KU3; -.
DR PDBsum; 1KU7; -.
DR PDBsum; 1L9U; -.
DR PDBsum; 1L9Z; -.
DR PDBsum; 1RIO; -.
DR PDBsum; 3LES; -.
DR PDBsum; 3LEV; -.
DR PDBsum; 3N97; -.
DR PDBsum; 3UGO; -.
DR PDBsum; 3UGP; -.
DR PDBsum; 4KI2; -.
DR PDBsum; 4XLN; -.
DR PDBsum; 4XLP; -.
DR PDBsum; 4XLQ; -.
DR PDBsum; 4XLR; -.
DR PDBsum; 4XLS; -.
DR PDBsum; 5TJG; -.
DR AlphaFoldDB; Q9EZJ8; -.
DR SMR; Q9EZJ8; -.
DR DIP; DIP-49014N; -.
DR IntAct; Q9EZJ8; 1.
DR EvolutionaryTrace; Q9EZJ8; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0016987; F:sigma factor activity; IDA:CACAO.
DR GO; GO:0006352; P:DNA-templated transcription, initiation; IEA:UniProtKB-UniRule.
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; PS00716; SIGMA70_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cytoplasm; Direct protein sequencing; DNA-binding;
KW Sigma factor; Transcription; Transcription regulation.
FT CHAIN 1..438
FT /note="RNA polymerase sigma factor SigA"
FT /id="PRO_0000423011"
FT DNA_BIND 398..417
FT /note="H-T-H motif"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00963"
FT REGION 1..69
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 93..128
FT /note="Sigma-70 factor domain-1"
FT REGION 202..272
FT /note="Sigma-70 factor domain-2"
FT REGION 281..359
FT /note="Sigma-70 factor domain-3"
FT REGION 372..424
FT /note="Sigma-70 factor domain-4"
FT MOTIF 226..229
FT /note="Interaction with polymerase core subunit RpoC"
FT COMPBIAS 10..30
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 31..63
FT /note="Acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT HELIX 94..103
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 111..135
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 139..148
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 151..153
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 168..179
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 183..204
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 207..214
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 215..217
FT /evidence="ECO:0007829|PDB:3UGO"
FT STRAND 220..222
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 224..241
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 244..246
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 250..269
FT /evidence="ECO:0007829|PDB:3UGO"
FT HELIX 277..297
FT /evidence="ECO:0007829|PDB:5TJG"
FT HELIX 303..310
FT /evidence="ECO:0007829|PDB:5TJG"
FT HELIX 316..326
FT /evidence="ECO:0007829|PDB:5TJG"
FT HELIX 344..346
FT /evidence="ECO:0007829|PDB:5TJG"
FT STRAND 351..353
FT /evidence="ECO:0007829|PDB:5TJG"
FT STRAND 370..372
FT /evidence="ECO:0007829|PDB:1KU3"
FT TURN 373..375
FT /evidence="ECO:0007829|PDB:1KU3"
FT HELIX 378..387
FT /evidence="ECO:0007829|PDB:1KU3"
FT TURN 388..392
FT /evidence="ECO:0007829|PDB:1KU3"
FT HELIX 398..405
FT /evidence="ECO:0007829|PDB:1KU3"
FT HELIX 409..425
FT /evidence="ECO:0007829|PDB:1KU3"
FT HELIX 434..437
FT /evidence="ECO:0007829|PDB:1KU7"
SQ SEQUENCE 438 AA; 49847 MW; 5D8ACF5713DE55AD CRC64;
MKKSKSKKKA AKAQEVEVKE PVKEPEPLPE LEAAEDLQDL PEPDPELLAS EPELEDLADP
LDLEGPLEAD LLPEEGLLEE EEEELSLPKV STSDPVRQYL HEIGQVPLLT LEEEIDLARK
VEEGMEAIKK LSEATGLDQE LIREVVRAKI LGTARIQKIP GLKEKPDPKT VEEVDGKLKS
LPKELKRYLH IAREGEAARQ HLIEANLRLV VSIAKKYTGR GLSFLDLIQE GNQGLIRAVE
KFEYKRRFKF STYATWWIRQ AINRAIADQA RTIRIPVHMV ETINKLSRTA RQLQQELGRE
PSYEEIAEAM GPGWDAKRVE ETLKIAQEPV SLETPIGDEK DSFYGDFIPD ENLPSPVEAA
AQSLLSEELE KALSKLSERE AMVLKLRKGL IDGREHTLEE VGAYFGVTRE RIRQIENKAL
RKLKYHESRT RKLRDFLE
