Structure of PDB 5w4u Chain B

Receptor sequence
>5w4uB (length=1089) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVFI
GRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSAISTLQVKLYGREGSSARTIKATLP
YIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVI
QDRETALDFIGRRGKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGY
MINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFR
YMQRTLAINAKTITSGLKYALATGNWGEQKKARAGVSQVLNRYTYSSTLS
HLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGT
DPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMET
LRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHK
ELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESILIAMQPE
DLEPDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRN
TYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFREL
PAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYG
MSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTP
ISKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFA
SRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLL
SKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKL
MAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFG
EMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFE
CKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDR
3D structure
PDB5w4u Epigenetic DNA Modification N6-Methyladenine Causes Site-Specific RNA Polymerase II Transcriptional Pausing.
ChainB
Resolution3.6 Å
3D
structure
Catalytic site residues are labeled in the structure
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Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D720
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 dna B Y459 A462 T791 R857 R1122 L1128 R1129 Y369 A372 T674 R740 R991 L997 R998
BS02 rna B Q776 K979 K987 H1097 Q659 K848 K856 H966
BS03 ZN B C1163 C1166 C1185 C1032 C1035 C1054
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:5w4u, PDBe:5w4u, PDBj:5w4u
PDBsum5w4u
PubMed28933854
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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