Structure of PDB 8ukt Chain B

Receptor sequence
>8uktB (length=1126) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILEQLARKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLF
VDVKKRTYESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGY
FIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFIS
TLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHIC
YDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRKEKRIQYAKDILQKE
FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLA
GPLLAQLFKTLFKKLTKDIFRYMQRTVEELAINAKTITSGLKYALATGNW
GEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLV
CPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPH
QSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREK
ELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDVEEY
TWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAELDVDPAKRIRVSHHA
TTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNY
NVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQ
EDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRM
KHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISAYHSKRDASTPLRSTE
NGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYR
REDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDAS
PFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRL
RHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAAS
FLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIH
IPYAAKLLFQELMAMNITPRLYTDRS
3D structure
PDB8ukt Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG.
ChainB
Resolution3.6 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 rna B G478 Q481 Q776 K979 K987 H1097 G412 Q415 Q691 K884 K892 H1002
BS02 dna B S208 K210 V482 T791 M792 R857 R942 G1121 R1122 R1129 M1133 S156 K158 V416 T706 M707 R772 R847 G1026 R1027 R1034 M1038
BS03 ZN B C1163 C1166 C1185 C1068 C1071 C1090
Gene Ontology
Molecular Function
GO:0001055 RNA polymerase II activity
GO:0003677 DNA binding
GO:0003729 mRNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0003968 RNA-dependent RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0001172 RNA-templated transcription
GO:0006351 DNA-templated transcription
GO:0006366 transcription by RNA polymerase II
GO:0006367 transcription initiation at RNA polymerase II promoter
GO:0006368 transcription elongation by RNA polymerase II
Cellular Component
GO:0000428 DNA-directed RNA polymerase complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005665 RNA polymerase II, core complex
GO:0005739 mitochondrion
GO:0010494 cytoplasmic stress granule

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ukt, PDBe:8ukt, PDBj:8ukt
PDBsum8ukt
PubMed38393762
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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