ID C4R7L2_KOMPG Unreviewed; 304 AA.
AC C4R7L2;
DT 07-JUL-2009, integrated into UniProtKB/TrEMBL.
DT 07-JUL-2009, sequence version 1.
DT 27-MAR-2024, entry version 85.
DE SubName: Full=RNA polymerase II third largest subunit B44, part of central core {ECO:0000313|EMBL:CAY71587.1};
GN OrderedLocusNames=PAS_chr4_0344 {ECO:0000313|EMBL:CAY71587.1};
OS Komagataella phaffii (strain GS115 / ATCC 20864) (Yeast) (Pichia pastoris).
OC Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes;
OC Saccharomycetales; Phaffomycetaceae; Komagataella.
OX NCBI_TaxID=644223 {ECO:0000313|EMBL:CAY71587.1, ECO:0000313|Proteomes:UP000000314};
RN [1] {ECO:0000313|EMBL:CAY71587.1, ECO:0000313|Proteomes:UP000000314}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GS115 / ATCC 20864 {ECO:0000313|Proteomes:UP000000314};
RX PubMed=19465926; DOI=10.1038/nbt.1544;
RA De Schutter K., Lin Y.C., Tiels P., Van Hecke A., Glinka S.,
RA Weber-Lehmann J., Rouze P., Van de Peer Y., Callewaert N.;
RT "Genome sequence of the recombinant protein production host Pichia
RT pastoris.";
RL Nat. Biotechnol. 27:561-566(2009).
RN [2] {ECO:0007829|PDB:5X4Z, ECO:0007829|PDB:5X50}
RP X-RAY CRYSTALLOGRAPHY (4.29 ANGSTROMS) IN COMPLEX WITH ZINC.
RX PubMed=28412353; DOI=10.1016/j.bbrc.2017.04.039;
RA Ehara H., Umehara T., Sekine S.I., Yokoyama S.;
RT "Crystal structure of RNA polymerase II from Komagataella pastoris.";
RL Biochem. Biophys. Res. Commun. 487:230-235(2017).
RN [3] {ECO:0007829|PDB:5XOG, ECO:0007829|PDB:5XON}
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) IN COMPLEX WITH ZINC.
RX PubMed=28775211; DOI=10.1126/science.aan8552;
RA Ehara H., Yokoyama T., Shigematsu H., Yokoyama S., Shirouzu M.,
RA Sekine S.I.;
RT "Structure of the complete elongation complex of RNA polymerase II with
RT basal factors.";
RL Science 357:921-924(2017).
RN [4] {ECO:0007829|PDB:6A5L, ECO:0007829|PDB:6A5O}
RP STRUCTURE BY ELECTRON MICROSCOPY (5.60 ANGSTROMS).
RX PubMed=30287617; DOI=10.1126/science.aau9904;
RA Kujirai T., Ehara H., Fujino Y., Shirouzu M., Sekine S.I., Kurumizaka H.;
RT "Structural basis of the nucleosome transition during RNA polymerase II
RT passage.";
RL Science 362:595-598(2018).
RN [5] {ECO:0007829|PDB:6IR9, ECO:0007829|PDB:6J4W}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.80 ANGSTROMS).
RX PubMed=30733384; DOI=10.1126/science.aav8912;
RA Ehara H., Kujirai T., Fujino Y., Shirouzu M., Kurumizaka H., Sekine S.I.;
RT "Structural insight into nucleosome transcription by RNA polymerase II with
RT elongation factors.";
RL Science 363:744-747(2019).
RN [6] {ECO:0007829|PDB:8H0V, ECO:0007829|PDB:8H0W}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.80 ANGSTROMS).
RX PubMed=36435862; DOI=10.1038/s41467-022-35003-z;
RA Hirano R., Ehara H., Kujirai T., Uejima T., Takizawa Y., Sekine S.I.,
RA Kurumizaka H.;
RT "Structural basis of RNA polymerase II transcription on the chromatosome
RT containing linker histone H1.";
RL Nat. Commun. 13:7287-7287(2022).
RN [7] {ECO:0007829|PDB:7XN7, ECO:0007829|PDB:7XSE}
RP STRUCTURE BY ELECTRON MICROSCOPY (3.10 ANGSTROMS).
RX PubMed=35981082; DOI=10.1126/science.abp9466;
RA Ehara H., Kujirai T., Shirouzu M., Kurumizaka H., Sekine S.I.;
RT "Structural basis of nucleosome disassembly and reassembly by RNAPII
RT elongation complex with FACT.";
RL Science 377:eabp9466-eabp9466(2022).
RN [8] {ECO:0007829|PDB:7WBV, ECO:0007829|PDB:7WBW}
RP STRUCTURE BY ELECTRON MICROSCOPY (4.00 ANGSTROMS).
RX PubMed=37120012; DOI=10.1016/j.jmb.2023.168130;
RA Osumi K., Kujirai T., Ehara H., Ogasawara M., Kinoshita C., Saotome M.,
RA Kagawa W., Sekine S.I., Takizawa Y., Kurumizaka H.;
RT "Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA
RT Polymerase II in the Nucleosome.";
RL J. Mol. Biol. 435:168130-168130(2023).
CC -!- SIMILARITY: Belongs to the archaeal Rpo3/eukaryotic RPB3 RNA polymerase
CC subunit family. {ECO:0000256|ARBA:ARBA00025804}.
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DR EMBL; FN392322; CAY71587.1; -; Genomic_DNA.
DR RefSeq; XP_002493766.1; XM_002493721.1.
DR PDB; 5X4Z; X-ray; 7.80 A; C/O=1-304.
DR PDB; 5X50; X-ray; 4.29 A; C=1-304.
DR PDB; 5X51; X-ray; 7.00 A; C/O=1-304.
DR PDB; 5XOG; X-ray; 3.00 A; C=1-304.
DR PDB; 5XON; EM; 3.83 A; C=1-304.
DR PDB; 6A5L; EM; 5.60 A; C=1-304.
DR PDB; 6A5O; EM; 9.90 A; C=1-304.
DR PDB; 6A5P; EM; 7.00 A; C=1-304.
DR PDB; 6A5R; EM; 8.70 A; C=1-304.
DR PDB; 6A5T; EM; 6.70 A; C=1-304.
DR PDB; 6A5U; EM; 7.60 A; C=1-304.
DR PDB; 6INQ; EM; 6.90 A; C=1-304.
DR PDB; 6IR9; EM; 3.80 A; C=1-304.
DR PDB; 6J4W; EM; 7.90 A; C=1-304.
DR PDB; 6J4X; EM; 4.30 A; C=1-304.
DR PDB; 6J4Y; EM; 4.30 A; C=1-304.
DR PDB; 6J4Z; EM; 4.10 A; C=1-304.
DR PDB; 6J50; EM; 4.70 A; C=1-304.
DR PDB; 6J51; EM; 4.20 A; C=1-304.
DR PDB; 7WBV; EM; 4.10 A; C=1-304.
DR PDB; 7WBW; EM; 7.10 A; C=1-304.
DR PDB; 7WBX; EM; 4.00 A; C=1-304.
DR PDB; 7XN7; EM; 3.10 A; C=1-304.
DR PDB; 7XSE; EM; 3.60 A; C=1-304.
DR PDB; 7XSX; EM; 3.80 A; C=1-304.
DR PDB; 7XSZ; EM; 3.40 A; C=1-304.
DR PDB; 7XT7; EM; 4.20 A; C=1-304.
DR PDB; 7XTD; EM; 3.90 A; C=1-304.
DR PDB; 7XTI; EM; 3.90 A; C=1-304.
DR PDB; 8H0V; EM; 3.80 A; C=1-304.
DR PDB; 8H0W; EM; 4.60 A; C=1-304.
DR PDB; 8HE5; EM; 6.95 A; C=1-304.
DR PDBsum; 5X4Z; -.
DR PDBsum; 5X50; -.
DR PDBsum; 5X51; -.
DR PDBsum; 5XOG; -.
DR PDBsum; 5XON; -.
DR PDBsum; 6A5L; -.
DR PDBsum; 6A5O; -.
DR PDBsum; 6A5P; -.
DR PDBsum; 6A5R; -.
DR PDBsum; 6A5T; -.
DR PDBsum; 6A5U; -.
DR PDBsum; 6INQ; -.
DR PDBsum; 6IR9; -.
DR PDBsum; 6J4W; -.
DR PDBsum; 6J4X; -.
DR PDBsum; 6J4Y; -.
DR PDBsum; 6J4Z; -.
DR PDBsum; 6J50; -.
DR PDBsum; 6J51; -.
DR AlphaFoldDB; C4R7L2; -.
DR EMDB; EMD-0671; -.
DR EMDB; EMD-0672; -.
DR EMDB; EMD-0673; -.
DR EMDB; EMD-0674; -.
DR EMDB; EMD-0675; -.
DR EMDB; EMD-0676; -.
DR EMDB; EMD-33313; -.
DR EMDB; EMD-33424; -.
DR EMDB; EMD-33436; -.
DR EMDB; EMD-33437; -.
DR EMDB; EMD-33441; -.
DR EMDB; EMD-33447; -.
DR EMDB; EMD-33450; -.
DR EMDB; EMD-34415; -.
DR EMDB; EMD-34416; -.
DR EMDB; EMD-36251; -.
DR EMDB; EMD-36252; -.
DR EMDB; EMD-36253; -.
DR EMDB; EMD-6747; -.
DR EMDB; EMD-6980; -.
DR EMDB; EMD-6981; -.
DR EMDB; EMD-6982; -.
DR EMDB; EMD-6983; -.
DR EMDB; EMD-6984; -.
DR EMDB; EMD-6985; -.
DR EMDB; EMD-6986; -.
DR EMDB; EMD-9713; -.
DR SMR; C4R7L2; -.
DR IntAct; C4R7L2; 4.
DR STRING; 644223.C4R7L2; -.
DR EnsemblFungi; CAY71587; CAY71587; PAS_chr4_0344.
DR GeneID; 8200785; -.
DR KEGG; ppa:PAS_chr4_0344; -.
DR eggNOG; KOG1522; Eukaryota.
DR HOGENOM; CLU_038421_1_1_1; -.
DR InParanoid; C4R7L2; -.
DR OMA; PENIVMM; -.
DR OrthoDB; 5472982at2759; -.
DR Proteomes; UP000000314; Chromosome 4.
DR GO; GO:0055029; C:nuclear DNA-directed RNA polymerase complex; IEA:UniProt.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003899; F:DNA-directed 5'-3' RNA polymerase activity; IEA:InterPro.
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:DNA-templated transcription; IEA:InterPro.
DR CDD; cd07031; RNAP_II_RPB3; 1.
DR Gene3D; 2.170.120.12; DNA-directed RNA polymerase, insert domain; 1.
DR Gene3D; 3.30.1360.10; RNA polymerase, RBP11-like subunit; 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 PANTHER; PTHR11800; DNA-DIRECTED RNA POLYMERASE; 1.
DR PANTHER; PTHR11800:SF2; DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3; 1.
DR Pfam; PF01000; RNA_pol_A_bac; 1.
DR Pfam; PF01193; RNA_pol_L; 1.
DR SMART; SM00662; RPOLD; 1.
DR SUPFAM; SSF56553; Insert subdomain of RNA polymerase alpha subunit; 1.
DR SUPFAM; SSF55257; RBP11-like subunits of RNA polymerase; 1.
DR PROSITE; PS00446; RNA_POL_D_30KD; 1.
PE 1: Evidence at protein level;
KW 3D-structure {ECO:0007829|PDB:5X4Z, ECO:0007829|PDB:5X50};
KW DNA-directed RNA polymerase {ECO:0000256|ARBA:ARBA00022478};
KW Metal-binding {ECO:0007829|PDB:5X4Z, ECO:0007829|PDB:5X50};
KW Reference proteome {ECO:0000313|Proteomes:UP000000314};
KW Transcription {ECO:0000256|ARBA:ARBA00023163};
KW Zinc {ECO:0007829|PDB:5X4Z, ECO:0007829|PDB:5X50}.
FT DOMAIN 16..261
FT /note="DNA-directed RNA polymerase RpoA/D/Rpb3-type"
FT /evidence="ECO:0000259|SMART:SM00662"
FT BINDING 82
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0007829|PDB:5X50"
FT BINDING 85
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007829|PDB:5X4Z, ECO:0007829|PDB:5X51"
FT BINDING 87
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007829|PDB:5X4Z, ECO:0007829|PDB:5X51"
FT BINDING 87
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0007829|PDB:5X50"
FT BINDING 91
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007829|PDB:5X4Z, ECO:0007829|PDB:5X51"
FT BINDING 94
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0007829|PDB:5X4Z, ECO:0007829|PDB:5X51"
FT BINDING 94
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0007829|PDB:5X50"
SQ SEQUENCE 304 AA; 34176 MW; 817B5BA131241412 CRC64;
MSKEPKVNII NAQDDEVELM LSDVNLSLAN SLRRTMLAEV PTLAIDLVEI KMNTSVLADE
FISHRLGLIP LVSEDVEEMK YSRDCTCEDY CDECSVVLEL SARHEGEEGT TDVYSSSLIK
VSGPGNLNVG EPVRRDDYDQ GILLCKLRNH QELNIRCIAK KGIAKEHAKW SPCSAIAFEY
DPHNKLKHTD FWFEVDAKKE WPDSKYATWE EPPKPGEVFD YKAKPNRFYM TVETTGSLKA
NQVFSRGIKT LQEKLANVLF ELENSRPANT TAYGGATAYG GQTVYGRETS YGGNTNYGDY
NAPY
//
