RPO3_SACSH
ID RPO3_SACSH Reviewed; 265 AA.
AC B8YB56;
DT 29-SEP-2021, integrated into UniProtKB/Swiss-Prot.
DT 03-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 67.
DE RecName: Full=DNA-directed RNA polymerase subunit Rpo3 {ECO:0000255|HAMAP-Rule:MF_00320, ECO:0000303|PubMed:19419240};
DE EC=2.7.7.6 {ECO:0000255|HAMAP-Rule:MF_00320};
DE AltName: Full=DNA-directed RNA polymerase subunit D {ECO:0000255|HAMAP-Rule:MF_00320};
GN Name=rpo3 {ECO:0000255|HAMAP-Rule:MF_00320, ECO:0000303|PubMed:19419240};
GN Synonyms=rpoD {ECO:0000255|HAMAP-Rule:MF_00320};
OS Saccharolobus shibatae (Sulfolobus shibatae).
OC Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae;
OC Saccharolobus.
OX NCBI_TaxID=2286;
RN [1] {ECO:0007744|PDB:2WAQ, ECO:0007744|PDB:2WB1}
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], X-RAY CRYSTALLOGRAPHY (3.35 ANGSTROMS)
RP OF THE RNA POLYMERASE COMPLEX IN COMPLEX WITH IRON-SULFUR (3FE-4S),
RP COFACTOR, SUBUNIT, AND NOMENCLATURE.
RC STRAIN=ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12;
RX PubMed=19419240; DOI=10.1371/journal.pbio.1000102;
RA Korkhin Y., Unligil U.M., Littlefield O., Nelson P.J., Stuart D.I.,
RA Sigler P.B., Bell S.D., Abrescia N.G.;
RT "Evolution of complex RNA polymerases: the complete archaeal RNA polymerase
RT structure.";
RL PLoS Biol. 7:e1000102-e1000102(2009).
RN [2] {ECO:0007744|PDB:2Y0S}
RP X-RAY CRYSTALLOGRAPHY (3.80 ANGSTROMS) OF THE RNA POLYMERASE COMPLEX IN
RP COMPLEX WITH IRON-SULFUR (3FE-4S), COFACTOR, AND SUBUNIT.
RC STRAIN=ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12;
RX PubMed=21265742; DOI=10.1042/bst0390025;
RA Wojtas M., Peralta B., Ondiviela M., Mogni M., Bell S.D., Abrescia N.G.;
RT "Archaeal RNA polymerase: the influence of the protruding stalk in crystal
RT packing and preliminary biophysical analysis of the Rpo13 subunit.";
RL Biochem. Soc. Trans. 39:25-30(2011).
RN [3] {ECO:0007744|PDB:4AYB, ECO:0007744|PDB:4V8S}
RP X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) OF THE RNA POLYMERASE COMPLEX IN
RP COMPLEX WITH IRON-SULFUR (3FE-4S) WITH AND WITHOUT DNA, COFACTOR, SUBUNIT,
RP AND SUBCELLULAR LOCATION.
RC STRAIN=ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12;
RX PubMed=22848102; DOI=10.1093/nar/gks692;
RA Wojtas M.N., Mogni M., Millet O., Bell S.D., Abrescia N.G.;
RT "Structural and functional analyses of the interaction of archaeal RNA
RT polymerase with DNA.";
RL Nucleic Acids Res. 40:9941-9952(2012).
CC -!- FUNCTION: DNA-dependent RNA polymerase (RNAP) catalyzes the
CC transcription of DNA into RNA using the four ribonucleoside
CC triphosphates as substrates. {ECO:0000255|HAMAP-Rule:MF_00320}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate +
CC RNA(n+1); Xref=Rhea:RHEA:21248, Rhea:RHEA-COMP:14527, Rhea:RHEA-
CC COMP:17342, ChEBI:CHEBI:33019, ChEBI:CHEBI:61557, ChEBI:CHEBI:140395;
CC EC=2.7.7.6; Evidence={ECO:0000255|HAMAP-Rule:MF_00320};
CC -!- COFACTOR:
CC Name=[3Fe-4S] cluster; Xref=ChEBI:CHEBI:21137;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00320,
CC ECO:0000269|PubMed:19419240, ECO:0000269|PubMed:21265742,
CC ECO:0000269|PubMed:22848102};
CC Note=Binds 1 [3Fe-4S] cluster. {ECO:0000255|HAMAP-Rule:MF_00320,
CC ECO:0000269|PubMed:19419240, ECO:0000269|PubMed:21265742,
CC ECO:0000269|PubMed:22848102};
CC -!- SUBUNIT: Part of the 13-subunit RNA polymerase complex.
CC {ECO:0000269|PubMed:19419240, ECO:0000269|PubMed:21265742,
CC ECO:0000269|PubMed:22848102}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00320,
CC ECO:0000269|PubMed:22848102}.
CC -!- SIMILARITY: Belongs to the archaeal Rpo3/eukaryotic RPB3 RNA polymerase
CC subunit family. {ECO:0000255|HAMAP-Rule:MF_00320}.
CC -!- CAUTION: X-ray crystallography in this and other archaea shows this
CC protein binds a 3Fe-4S cluster, although a 4Fe-4S cluster has been
CC suggested to be present in this protein. {ECO:0000269|PubMed:19419240,
CC ECO:0000269|PubMed:21265742, ECO:0000269|PubMed:22848102, ECO:0000305}.
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DR EMBL; FJ515668; ACL36491.1; -; Genomic_DNA.
DR PDB; 2WAQ; X-ray; 3.35 A; D=1-265.
DR PDB; 2WB1; X-ray; 3.52 A; D/S=1-265.
DR PDB; 2Y0S; X-ray; 3.80 A; D/S=1-265.
DR PDB; 4AYB; X-ray; 3.20 A; D=1-265.
DR PDB; 4V8S; X-ray; 4.32 A; AS/BD=1-265.
DR PDBsum; 2WAQ; -.
DR PDBsum; 2WB1; -.
DR PDBsum; 2Y0S; -.
DR PDBsum; 4AYB; -.
DR PDBsum; 4V8S; -.
DR SMR; B8YB56; -.
DR BRENDA; 2.7.7.6; 6162.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0000428; C:DNA-directed RNA polymerase complex; IDA:UniProtKB.
DR GO; GO:0051538; F:3 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0046983; F:protein dimerization activity; IEA:InterPro.
DR GO; GO:0006351; P:transcription, DNA-templated; IEA:UniProtKB-UniRule.
DR Gene3D; 2.170.120.12; -; 1.
DR Gene3D; 3.30.1360.10; -; 1.
DR HAMAP; MF_00320; RNApol_arch_Rpo3; 1.
DR InterPro; IPR001514; DNA-dir_RNA_pol_30-40kDasu_CS.
DR InterPro; IPR011262; DNA-dir_RNA_pol_insert.
DR InterPro; IPR011263; DNA-dir_RNA_pol_RpoA/D/Rpb3.
DR InterPro; IPR036603; RBP11-like.
DR InterPro; IPR022842; RNAP_Rpo3/Rpb3/RPAC1.
DR InterPro; IPR036643; RNApol_insert_sf.
DR Pfam; PF01000; RNA_pol_A_bac; 1.
DR Pfam; PF01193; RNA_pol_L; 1.
DR SMART; SM00662; RPOLD; 1.
DR SUPFAM; SSF55257; SSF55257; 1.
DR SUPFAM; SSF56553; SSF56553; 1.
DR PROSITE; PS00446; RNA_POL_D_30KD; 1.
PE 1: Evidence at protein level;
KW 3D-structure; 3Fe-4S; Cytoplasm; DNA-directed RNA polymerase; Iron;
KW Iron-sulfur; Metal-binding; Nucleotidyltransferase; Transcription;
KW Transferase.
FT CHAIN 1..265
FT /note="DNA-directed RNA polymerase subunit Rpo3"
FT /id="PRO_0000453787"
FT BINDING 203
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00320,
FT ECO:0000269|PubMed:19419240, ECO:0007744|PDB:2WAQ,
FT ECO:0007744|PDB:2WB1, ECO:0007744|PDB:2Y0S,
FT ECO:0007744|PDB:4AYB"
FT BINDING 206
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00320,
FT ECO:0000269|PubMed:19419240, ECO:0007744|PDB:2WAQ,
FT ECO:0007744|PDB:2WB1, ECO:0007744|PDB:2Y0S,
FT ECO:0007744|PDB:4AYB"
FT BINDING 209
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00320,
FT ECO:0000269|PubMed:19419240, ECO:0007744|PDB:2WAQ,
FT ECO:0007744|PDB:2WB1, ECO:0007744|PDB:2Y0S,
FT ECO:0007744|PDB:4AYB"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 10..20
FT /evidence="ECO:0007829|PDB:4AYB"
FT HELIX 22..33
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 34..48
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:4AYB"
FT HELIX 55..64
FT /evidence="ECO:0007829|PDB:4AYB"
FT HELIX 72..75
FT /evidence="ECO:0007829|PDB:4AYB"
FT TURN 79..81
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 82..84
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 91..101
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 108..110
FT /evidence="ECO:0007829|PDB:4AYB"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 129..132
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 138..149
FT /evidence="ECO:0007829|PDB:4AYB"
FT TURN 150..152
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 153..156
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 159..168
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 171..174
FT /evidence="ECO:0007829|PDB:4AYB"
FT HELIX 177..182
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 184..186
FT /evidence="ECO:0007829|PDB:2WAQ"
FT STRAND 191..194
FT /evidence="ECO:0007829|PDB:4AYB"
FT HELIX 208..212
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 213..215
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 221..232
FT /evidence="ECO:0007829|PDB:4AYB"
FT STRAND 234..236
FT /evidence="ECO:0007829|PDB:4AYB"
FT HELIX 238..261
FT /evidence="ECO:0007829|PDB:4AYB"
SQ SEQUENCE 265 AA; 30142 MW; C9B868DD3DE305D0 CRC64;
MSINLLHKDD KRIDLVFEGY PLEFVNAIRR AAMLYVPVMS IDDVYFIENN SPLYDEILAH
RLALIPFTSE EALDTYRWPE ECIDCTENCE KCYTKIYIEA EALNEPKMLY SKDIKSEDPS
IVPISGDIPI VLLGANQKIS LEARLRLGYG KEHAKFIPVS LAIVRYYPKV EILGNCEKGA
TVCPEGVFEL KDGKLSVKNE LACTLCEECL RYCNGLIRIS SVEDKYILEL ESVGSLKPER
ILLEAGKSII RKIEELEKKL VEVIK
