Structure of PDB 6upy Chain B

Receptor sequence
>6upyB (length=1109) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKR
TKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVL
IAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGRE
GSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLE
MLKPCVEDGFVIQDRETALDFIGKEKRIQYAKDILQKEFLPHITQLEGFE
SRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLF
KKLTKDIFRYMQRTVEELAINAKTITSGLKYALATGNWGEQKKAMSSRAG
VSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACG
LVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNG
VWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVY
RPLFIVEDDGHKELKVRKGHIAKLMATEYQDVEEYTWSSLLNEGLVEYID
AEEEESILIAMQPEDLEPLDVDPAKRIRVSHHATTFTHCEIHPSMILGVA
ASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKP
LGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFR
SLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPG
VRVSGEDVIIGKTTPISAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLK
FVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLII
NPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREH
GYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQ
VLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHI
CGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNI
TPRLYTDRS
3D structure
PDB6upy RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair-pi and CH-pi interactions.
ChainB
Resolution3.4 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 Q481 P528 Q776 K979 K987 H1097 Q403 P444 Q674 K867 K875 H985
BS02 dna B S208 K210 M792 R857 R1122 S1123 R1129 M1133 S146 K148 M690 R755 R1010 S1011 R1017 M1021
BS03 APC B S1019 R1020 S907 R908
BS04 ZN B C1163 C1166 C1182 C1185 C1051 C1054 C1070 C1073
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:6upy, PDBe:6upy, PDBj:6upy
PDBsum6upy
PubMed32284409
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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