RPO3_SACS2
ID RPO3_SACS2 Reviewed; 265 AA.
AC P95989;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1997, sequence version 1.
DT 03-AUG-2022, entry version 144.
DE RecName: Full=DNA-directed RNA polymerase subunit Rpo3 {ECO:0000255|HAMAP-Rule:MF_00320};
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, ECO:0000303|PubMed:18235446};
GN Name=rpo3 {ECO:0000255|HAMAP-Rule:MF_00320};
GN Synonyms=rpoD {ECO:0000255|HAMAP-Rule:MF_00320,
GN ECO:0000303|PubMed:11427726}; OrderedLocusNames=SSO0071;
GN ORFNames=C04_051 {ECO:0000303|PubMed:8899719};
OS Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
OS (Sulfolobus solfataricus).
OC Archaea; Crenarchaeota; Thermoprotei; Sulfolobales; Sulfolobaceae;
OC Saccharolobus.
OX NCBI_TaxID=273057;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 35092 / DSM 1617 / JCM 11322 / P2;
RX PubMed=8899719; DOI=10.1111/j.1365-2958.1996.tb02666.x;
RA Sensen C.W., Klenk H.-P., Singh R.K., Allard G., Chan C.C.-Y., Liu Q.Y.,
RA Penny S.L., Young F., Schenk M.E., Gaasterland T., Doolittle W.F.,
RA Ragan M.A., Charlebois R.L.;
RT "Organizational characteristics and information content of an archaeal
RT genome: 156 kb of sequence from Sulfolobus solfataricus P2.";
RL Mol. Microbiol. 22:175-191(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35092 / DSM 1617 / JCM 11322 / P2;
RX PubMed=11427726; DOI=10.1073/pnas.141222098;
RA She Q., Singh R.K., Confalonieri F., Zivanovic Y., Allard G., Awayez M.J.,
RA Chan-Weiher C.C.-Y., Clausen I.G., Curtis B.A., De Moors A., Erauso G.,
RA Fletcher C., Gordon P.M.K., Heikamp-de Jong I., Jeffries A.C., Kozera C.J.,
RA Medina N., Peng X., Thi-Ngoc H.P., Redder P., Schenk M.E., Theriault C.,
RA Tolstrup N., Charlebois R.L., Doolittle W.F., Duguet M., Gaasterland T.,
RA Garrett R.A., Ragan M.A., Sensen C.W., Van der Oost J.;
RT "The complete genome of the crenarchaeon Sulfolobus solfataricus P2.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:7835-7840(2001).
RN [3] {ECO:0007744|PDB:2PA8, ECO:0007744|PDB:2PMZ, ECO:0007744|PDB:3HKZ}
RP X-RAY CRYSTALLOGRAPHY (3.40 ANGSTROMS) OF THE RNA POLYMERASE COMPLEX IN
RP COMPLEX WITH IRON-SULFUR (3FE-4S), X-RAY CRYSTALLOGRAPHY (1.76 ANGSTROMS)
RP IN COMPLEX WITH RPO11 AND IRON-SULFUR (3FE-4S), IRON-SULFUR-BINDING,
RP COFACTOR, SUBUNIT, AND MUTAGENESIS OF CYS-183; CYS-203; CYS-206 AND
RP CYS-209.
RC STRAIN=ATCC 35092 / DSM 1617 / JCM 11322 / P2;
RX PubMed=18235446; DOI=10.1038/nature06530;
RA Hirata A., Klein B.J., Murakami K.S.;
RT "The X-ray crystal structure of RNA polymerase from Archaea.";
RL Nature 451:851-854(2008).
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:18235446};
CC Note=Binds 1 [3Fe-4S] cluster. {ECO:0000255|HAMAP-Rule:MF_00320,
CC ECO:0000269|PubMed:18235446};
CC -!- SUBUNIT: Part of the 13-subunit RNA polymerase complex.
CC {ECO:0000269|PubMed:18235446}.
CC -!- INTERACTION:
CC P95989; Q980K0: rpo11; NbExp=2; IntAct=EBI-9022065, EBI-9022031;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00320}.
CC -!- DOMAIN: The presence of the iron-sulfur cluster is required for
CC assembly of the RNA polymerase complex. {ECO:0000269|PubMed:18235446}.
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:18235446,
CC ECO:0000305}.
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DR EMBL; Y08257; CAA69531.1; -; Genomic_DNA.
DR EMBL; AE006641; AAK40433.1; -; Genomic_DNA.
DR PIR; S75417; S75417.
DR RefSeq; WP_009988881.1; NC_002754.1.
DR PDB; 2PA8; X-ray; 1.76 A; D=1-265.
DR PDB; 2PMZ; X-ray; 3.40 A; D/S=1-265.
DR PDB; 3HKZ; X-ray; 3.40 A; D/O=1-265.
DR PDBsum; 2PA8; -.
DR PDBsum; 2PMZ; -.
DR PDBsum; 3HKZ; -.
DR AlphaFoldDB; P95989; -.
DR SMR; P95989; -.
DR DIP; DIP-60646N; -.
DR IntAct; P95989; 2.
DR STRING; 273057.SSO0071; -.
DR EnsemblBacteria; AAK40433; AAK40433; SSO0071.
DR GeneID; 44129034; -.
DR KEGG; sso:SSO0071; -.
DR PATRIC; fig|273057.12.peg.72; -.
DR eggNOG; arCOG04241; Archaea.
DR HOGENOM; CLU_038421_3_1_2; -.
DR InParanoid; P95989; -.
DR OMA; ECLRHPE; -.
DR PhylomeDB; P95989; -.
DR BRENDA; 2.7.7.6; 6163.
DR EvolutionaryTrace; P95989; -.
DR Proteomes; UP000001974; Chromosome.
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; Reference proteome;
KW Transcription; Transferase.
FT CHAIN 1..265
FT /note="DNA-directed RNA polymerase subunit Rpo3"
FT /id="PRO_0000132765"
FT BINDING 183
FT /ligand="[3Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:21137"
FT /evidence="ECO:0000305|PubMed:18235446"
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:18235446, ECO:0007744|PDB:2PA8,
FT ECO:0007744|PDB:2PMZ, ECO:0007744|PDB:3HKZ"
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:18235446, ECO:0007744|PDB:2PA8,
FT ECO:0007744|PDB:3HKZ"
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:18235446, ECO:0007744|PDB:2PA8,
FT ECO:0007744|PDB:2PMZ, ECO:0007744|PDB:3HKZ"
FT MUTAGEN 183
FT /note="C->S: Abolishes iron-sulfur-binding, causing
FT aggregation of Rpo3 and preventing the functional Rpo3-
FT Rpo11 subcomplex from being formed; when associated with S-
FT 203; S-206 and S-209."
FT /evidence="ECO:0000269|PubMed:18235446"
FT MUTAGEN 203
FT /note="C->S: Abolishes iron-sulfur-binding, causing
FT aggregation of Rpo3 and preventing the functional Rpo3-
FT Rpo11 subcomplex from being formed; when associated with S-
FT 183; S-206 and S-209."
FT /evidence="ECO:0000269|PubMed:18235446"
FT MUTAGEN 206
FT /note="C->S: Abolishes iron-sulfur-binding, causing
FT aggregation of Rpo3 and preventing the functional Rpo3-
FT Rpo11 subcomplex from being formed; when associated with S-
FT 183; S-203 and S-209."
FT /evidence="ECO:0000269|PubMed:18235446"
FT MUTAGEN 209
FT /note="C->S: Abolishes iron-sulfur-binding, causing
FT aggregation of Rpo3 and preventing the functional Rpo3-
FT Rpo11 subcomplex from being formed; when associated with S-
FT 183; S-203 and S-206."
FT /evidence="ECO:0000269|PubMed:18235446"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 10..20
FT /evidence="ECO:0007829|PDB:2PA8"
FT HELIX 22..34
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 38..49
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 51..53
FT /evidence="ECO:0007829|PDB:2PA8"
FT HELIX 55..62
FT /evidence="ECO:0007829|PDB:2PA8"
FT HELIX 72..75
FT /evidence="ECO:0007829|PDB:2PA8"
FT HELIX 79..81
FT /evidence="ECO:0007829|PDB:2PA8"
FT TURN 90..92
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 93..101
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 103..105
FT /evidence="ECO:0007829|PDB:2PMZ"
FT STRAND 107..110
FT /evidence="ECO:0007829|PDB:2PA8"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 129..133
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 138..148
FT /evidence="ECO:0007829|PDB:2PA8"
FT TURN 150..152
FT /evidence="ECO:0007829|PDB:2PA8"
FT HELIX 154..156
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 159..172
FT /evidence="ECO:0007829|PDB:2PA8"
FT HELIX 179..182
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 188..191
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 194..198
FT /evidence="ECO:0007829|PDB:2PA8"
FT HELIX 200..202
FT /evidence="ECO:0007829|PDB:2PA8"
FT HELIX 208..213
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 216..232
FT /evidence="ECO:0007829|PDB:2PA8"
FT STRAND 234..236
FT /evidence="ECO:0007829|PDB:2PA8"
FT HELIX 238..263
FT /evidence="ECO:0007829|PDB:2PA8"
SQ SEQUENCE 265 AA; 30294 MW; C5B9B863A78250AA CRC64;
MSINLLHKDD TRIDLVFEGY PLEFVNAIRR ASMLYVPIMA VDDVYFIENN SPLYDEILAH
RLALIPFMSE EALDTYRWPE ECIECTENCE KCYTKIYIEA EAPNEPRMIY SKDIKSEDPS
VVPISGDIPI VLLGTNQKIS LEARLRLGYG KEHAKFIPVS LSVVRYYPKV EILANCEKAV
NVCPEGVFEL KDGKLSVKNE LSCTLCEECL RYCNGSIRIS FVEDKYILEI ESVGSLKPER
ILLEAGKSII RKIEELEKKL VEVVK
