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Protein

DNA-directed RNA polymerase subunit D

Gene

rpoD

Organism
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates.

Catalytic activityi

Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).

Cofactori

[4Fe-4S] cluster1 PublicationNote: Binds 1 [4Fe-4S] cluster.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi183Iron-sulfur (4Fe-4S)1 Publication1
Metal bindingi203Iron-sulfur (4Fe-4S)1 Publication1
Metal bindingi206Iron-sulfur (4Fe-4S)1 Publication1
Metal bindingi209Iron-sulfur (4Fe-4S)1 Publication1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Transferase

Keywords - Biological processi

Transcription

Keywords - Ligandi

4Fe-4S, Iron, Iron-sulfur, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-directed RNA polymerase subunit D (EC:2.7.7.6)
Gene namesi
Name:rpoD
Ordered Locus Names:SSO0071
ORF Names:C04_051
OrganismiSulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Taxonomic identifieri273057 [NCBI]
Taxonomic lineageiArchaeaCrenarchaeotaThermoproteiSulfolobalesSulfolobaceaeSulfolobus
Proteomesi
  • UP000001974 Componenti: Chromosome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

DNA-directed RNA polymerase

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi183C → S: Abolishes iron-sulfur-binding, causing aggregation of RpoD and preventing the functional RpoD-RpoL subcomplex from being formed; when associated with S-203; S-206 and S-209. 1 Publication1
Mutagenesisi203C → S: Abolishes iron-sulfur-binding, causing aggregation of RpoD and preventing the functional RpoD-RpoL subcomplex from being formed; when associated with S-183; S-206 and S-209. 1 Publication1
Mutagenesisi206C → S: Abolishes iron-sulfur-binding, causing aggregation of RpoD and preventing the functional RpoD-RpoL subcomplex from being formed; when associated with S-183; S-203 and S-209. 1 Publication1
Mutagenesisi209C → S: Abolishes iron-sulfur-binding, causing aggregation of RpoD and preventing the functional RpoD-RpoL subcomplex from being formed; when associated with S-183; S-203 and S-206. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001327651 – 265DNA-directed RNA polymerase subunit DAdd BLAST265

Interactioni

Protein-protein interaction databases

DIPiDIP-60646N.
STRINGi273057.SSO0071.

Structurei

Secondary structure

1265
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 8Combined sources6
Beta strandi10 – 20Combined sources11
Helixi22 – 34Combined sources13
Beta strandi38 – 49Combined sources12
Beta strandi51 – 53Combined sources3
Helixi55 – 62Combined sources8
Helixi72 – 75Combined sources4
Helixi79 – 81Combined sources3
Turni90 – 92Combined sources3
Beta strandi93 – 101Combined sources9
Beta strandi103 – 105Combined sources3
Beta strandi107 – 110Combined sources4
Helixi111 – 113Combined sources3
Beta strandi115 – 118Combined sources4
Beta strandi129 – 133Combined sources5
Beta strandi138 – 148Combined sources11
Turni150 – 152Combined sources3
Helixi154 – 156Combined sources3
Beta strandi159 – 172Combined sources14
Helixi179 – 182Combined sources4
Beta strandi188 – 191Combined sources4
Beta strandi194 – 198Combined sources5
Helixi200 – 202Combined sources3
Helixi208 – 213Combined sources6
Beta strandi216 – 232Combined sources17
Beta strandi234 – 236Combined sources3
Helixi238 – 263Combined sources26

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2PA8X-ray1.76D1-265[»]
2PMZX-ray3.40D/S1-265[»]
3HKZX-ray3.40D/O1-265[»]
ProteinModelPortaliP95989.
SMRiP95989.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP95989.

Family & Domainsi

Domaini

The presence of the 4Fe-4S iron-sulfur is required for assembly of the RNA polymerase complex.1 Publication

Sequence similaritiesi

Phylogenomic databases

eggNOGiarCOG04241. Archaea.
COG0202. LUCA.
HOGENOMiHOG000230844.
InParanoidiP95989.
KOiK03047.
OMAiMAVDEVY.

Family and domain databases

Gene3Di2.170.120.12. 1 hit.
HAMAPiMF_00320. RNApol_arch_D. 1 hit.
InterProiIPR001514. DNA-dir_RNA_pol_30-40kDasu_CS.
IPR011262. DNA-dir_RNA_pol_insert.
IPR011263. DNA-dir_RNA_pol_RpoA/D/Rpb3.
IPR009025. RBP11-like_dimer.
IPR022842. RNAP_D.
[Graphical view]
PfamiPF01000. RNA_pol_A_bac. 1 hit.
PF01193. RNA_pol_L. 1 hit.
[Graphical view]
SMARTiSM00662. RPOLD. 1 hit.
[Graphical view]
SUPFAMiSSF55257. SSF55257. 2 hits.
SSF56553. SSF56553. 1 hit.
PROSITEiPS00446. RNA_POL_D_30KD. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P95989-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSINLLHKDD TRIDLVFEGY PLEFVNAIRR ASMLYVPIMA VDDVYFIENN
60 70 80 90 100
SPLYDEILAH RLALIPFMSE EALDTYRWPE ECIECTENCE KCYTKIYIEA
110 120 130 140 150
EAPNEPRMIY SKDIKSEDPS VVPISGDIPI VLLGTNQKIS LEARLRLGYG
160 170 180 190 200
KEHAKFIPVS LSVVRYYPKV EILANCEKAV NVCPEGVFEL KDGKLSVKNE
210 220 230 240 250
LSCTLCEECL RYCNGSIRIS FVEDKYILEI ESVGSLKPER ILLEAGKSII
260
RKIEELEKKL VEVVK
Length:265
Mass (Da):30,294
Last modified:May 1, 1997 - v1
Checksum:iC5B9B863A78250AA
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08257 Genomic DNA. Translation: CAA69531.1.
AE006641 Genomic DNA. Translation: AAK40433.1.
PIRiS75417.
RefSeqiWP_009988881.1. NC_002754.1.

Genome annotation databases

EnsemblBacteriaiAAK40433; AAK40433; SSO0071.
GeneIDi27426367.
KEGGisso:SSO0071.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y08257 Genomic DNA. Translation: CAA69531.1.
AE006641 Genomic DNA. Translation: AAK40433.1.
PIRiS75417.
RefSeqiWP_009988881.1. NC_002754.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2PA8X-ray1.76D1-265[»]
2PMZX-ray3.40D/S1-265[»]
3HKZX-ray3.40D/O1-265[»]
ProteinModelPortaliP95989.
SMRiP95989.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

DIPiDIP-60646N.
STRINGi273057.SSO0071.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAK40433; AAK40433; SSO0071.
GeneIDi27426367.
KEGGisso:SSO0071.

Phylogenomic databases

eggNOGiarCOG04241. Archaea.
COG0202. LUCA.
HOGENOMiHOG000230844.
InParanoidiP95989.
KOiK03047.
OMAiMAVDEVY.

Miscellaneous databases

EvolutionaryTraceiP95989.

Family and domain databases

Gene3Di2.170.120.12. 1 hit.
HAMAPiMF_00320. RNApol_arch_D. 1 hit.
InterProiIPR001514. DNA-dir_RNA_pol_30-40kDasu_CS.
IPR011262. DNA-dir_RNA_pol_insert.
IPR011263. DNA-dir_RNA_pol_RpoA/D/Rpb3.
IPR009025. RBP11-like_dimer.
IPR022842. RNAP_D.
[Graphical view]
PfamiPF01000. RNA_pol_A_bac. 1 hit.
PF01193. RNA_pol_L. 1 hit.
[Graphical view]
SMARTiSM00662. RPOLD. 1 hit.
[Graphical view]
SUPFAMiSSF55257. SSF55257. 2 hits.
SSF56553. SSF56553. 1 hit.
PROSITEiPS00446. RNA_POL_D_30KD. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiRPOD_SULSO
AccessioniPrimary (citable) accession number: P95989
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: May 1, 1997
Last modified: November 2, 2016
This is version 119 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.