Structure of PDB 8ukr Chain B

Receptor sequence
>8ukrB (length=1123) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILEQLARKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLF
VDVKKRTYESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGY
FIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFIS
TLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHIC
YDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRKEKRIQYAKDILQKE
FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLA
GPLLAQLFKTLFKKLTKDIFRYMQRTVEELAINAKTITSGLKYALATGNW
GEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLV
CPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPH
QSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREK
ELKIFTDAGRVYRPLFIVEDDGHKELKVRKGHIAKLMATEYQDVEEYTWS
SLLNEGLVEYIDAEEEESILIAMQPEDLEPAELDVDPAKRIRVSHHATTF
THCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVR
MDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDS
MIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHG
TYDKLDDDGLIAPGVRVSGEDVIIGKTTPISAYHSKRDASTPLRSTENGI
VDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRRED
MPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFT
DITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHM
VDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLK
ERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPY
AAKLLFQELMAMNITPRLYTDRS
3D structure
PDB8ukr Molecular Mechanism of RNA Polymerase II Transcriptional Mutagenesis by the Epimerizable DNA Lesion, Fapy·dG.
ChainB
Resolution3.78 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 A477 Q481 Q776 K987 H1097 A411 Q415 Q688 K889 H999
BS02 dna B A462 T791 M792 R942 G1121 R1122 R1129 A396 T703 M704 R844 G1023 R1024 R1031
BS03 ZN B C1163 C1166 C1182 C1185 C1065 C1068 C1084 C1087
BS04 ATP B R766 D837 S1019 R1020 R678 D749 S921 R922
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
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Biological Process
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Cellular Component
External links
PDB RCSB:8ukr, PDBe:8ukr, PDBj:8ukr
PDBsum8ukr
PubMed38393762
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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