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P95989

- RPOD_SULSO

UniProt

P95989 - RPOD_SULSO

Protein

DNA-directed RNA polymerase subunit D

Gene

rpoD

Organism
Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 104 (01 Oct 2014)
      Sequence version 1 (01 May 1997)
      Previous versions | rss
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    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

    Binds 1 4Fe-4S cluster.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi183 – 1831Iron-sulfur (4Fe-4S)1 Publication
    Metal bindingi203 – 2031Iron-sulfur (4Fe-4S)1 Publication
    Metal bindingi206 – 2061Iron-sulfur (4Fe-4S)1 Publication
    Metal bindingi209 – 2091Iron-sulfur (4Fe-4S)1 Publication

    GO - Molecular functioni

    1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
    2. DNA binding Source: UniProtKB-HAMAP
    3. DNA-directed RNA polymerase activity Source: UniProtKB-HAMAP
    4. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. transcription, DNA-templated Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    Transcription

    Keywords - Ligandi

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

    Enzyme and pathway databases

    BioCyciSSOL273057:GCH2-70-MONOMER.

    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
    ProteomesiUP000001974: Chromosome

    Subcellular locationi

    Keywords - Cellular componenti

    DNA-directed RNA polymerase

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi183 – 1831C → 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 Publication
    Mutagenesisi203 – 2031C → 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 Publication
    Mutagenesisi206 – 2061C → 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 Publication
    Mutagenesisi209 – 2091C → 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 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 265265DNA-directed RNA polymerase subunit DPRO_0000132765Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    DIPiDIP-60646N.
    STRINGi273057.SSO0071.

    Structurei

    Secondary structure

    1
    265
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 86
    Beta strandi10 – 2011
    Helixi22 – 3413
    Beta strandi38 – 4912
    Beta strandi51 – 533
    Helixi55 – 628
    Helixi72 – 754
    Helixi79 – 813
    Turni90 – 923
    Beta strandi93 – 1019
    Beta strandi103 – 1053
    Beta strandi107 – 1104
    Helixi111 – 1133
    Beta strandi115 – 1184
    Beta strandi129 – 1335
    Beta strandi138 – 14811
    Turni150 – 1523
    Helixi154 – 1563
    Beta strandi159 – 17214
    Helixi179 – 1824
    Beta strandi188 – 1914
    Beta strandi194 – 1985
    Helixi200 – 2023
    Helixi208 – 2136
    Beta strandi216 – 23217
    Beta strandi234 – 2363
    Helixi238 – 26326

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2PA8X-ray1.76D1-265[»]
    2PMZX-ray3.40D/S1-265[»]
    3HKZX-ray3.40D/O1-265[»]
    ProteinModelPortaliP95989.
    SMRiP95989. Positions 2-265.
    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

    eggNOGiCOG0202.
    HOGENOMiHOG000230844.
    KOiK03047.
    OMAiSVAAHRY.

    Family and domain databases

    Gene3Di2.170.120.12. 1 hit.
    HAMAPiMF_00320. RNApol_arch_D.
    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

    MSINLLHKDD TRIDLVFEGY PLEFVNAIRR ASMLYVPIMA VDDVYFIENN    50
    SPLYDEILAH RLALIPFMSE EALDTYRWPE ECIECTENCE KCYTKIYIEA 100
    EAPNEPRMIY SKDIKSEDPS VVPISGDIPI VLLGTNQKIS LEARLRLGYG 150
    KEHAKFIPVS LSVVRYYPKV EILANCEKAV NVCPEGVFEL KDGKLSVKNE 200
    LSCTLCEECL RYCNGSIRIS FVEDKYILEI ESVGSLKPER ILLEAGKSII 250
    RKIEELEKKL VEVVK 265
    Length:265
    Mass (Da):30,294
    Last modified:May 1, 1997 - v1
    Checksum:iC5B9B863A78250AA
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y08257 Genomic DNA. Translation: CAA69531.1.
    AE006641 Genomic DNA. Translation: AAK40433.1.
    PIRiS75417.
    RefSeqiNP_341643.1. NC_002754.1.

    Genome annotation databases

    EnsemblBacteriaiAAK40433; AAK40433; SSO0071.
    GeneIDi1455324.
    KEGGisso:SSO0071.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y08257 Genomic DNA. Translation: CAA69531.1 .
    AE006641 Genomic DNA. Translation: AAK40433.1 .
    PIRi S75417.
    RefSeqi NP_341643.1. NC_002754.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2PA8 X-ray 1.76 D 1-265 [» ]
    2PMZ X-ray 3.40 D/S 1-265 [» ]
    3HKZ X-ray 3.40 D/O 1-265 [» ]
    ProteinModelPortali P95989.
    SMRi P95989. Positions 2-265.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-60646N.
    STRINGi 273057.SSO0071.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAK40433 ; AAK40433 ; SSO0071 .
    GeneIDi 1455324.
    KEGGi sso:SSO0071.

    Phylogenomic databases

    eggNOGi COG0202.
    HOGENOMi HOG000230844.
    KOi K03047.
    OMAi SVAAHRY.

    Enzyme and pathway databases

    BioCyci SSOL273057:GCH2-70-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P95989.

    Family and domain databases

    Gene3Di 2.170.120.12. 1 hit.
    HAMAPi MF_00320. RNApol_arch_D.
    InterProi IPR001514. 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 ]
    Pfami PF01000. RNA_pol_A_bac. 1 hit.
    PF01193. RNA_pol_L. 1 hit.
    [Graphical view ]
    SMARTi SM00662. RPOLD. 1 hit.
    [Graphical view ]
    SUPFAMi SSF55257. SSF55257. 2 hits.
    SSF56553. SSF56553. 1 hit.
    PROSITEi PS00446. RNA_POL_D_30KD. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2."
      Sensen C.W., Klenk H.-P., Singh R.K., Allard G., Chan C.C.-Y., Liu Q.Y., Penny S.L., Young F., Schenk M.E., Gaasterland T., Doolittle W.F., Ragan M.A., Charlebois R.L.
      Mol. Microbiol. 22:175-191(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2.
    3. "The X-ray crystal structure of RNA polymerase from Archaea."
      Hirata A., Klein B.J., Murakami K.S.
      Nature 451:851-854(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.76 ANGSTROMS) OF THE RNA POLYMERASE COMPLEX IN COMPLEX WITH IRON, IRON-SULFUR-BINDING, COFACTOR, MUTAGENESIS OF CYS-183; CYS-203; CYS-206 AND CYS-209.

    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: October 1, 2014
    This is version 104 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

    External Data

    Dasty 3