Structure of PDB 2yu9 Chain B Binding Site BS01

Receptor Information
>2yu9 Chain B (length=1121) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTY
EAIDKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSE
KVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLY
GREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQ
MLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKE
FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLA
GPLLAQLFKTLFKKLTKDIFRYMQRTVELAINAKTITSGLKYALATGNWG
EQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVC
PAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQ
SPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKE
LKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWS
SLLNEGLVEYIDAEEEESILIAMQPEDLEPADVDPAKRIRVSHHATTFTH
CEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMD
TMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMI
MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTY
DKLDDDGLIAPGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVL
VTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTA
EGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVE
GISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKI
HARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLME
ASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLL
FQELMAMNITPRLYTDRSRDF
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB2yu9 Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis
Resolution3.4 Å
Binding residue
(original residue number in PDB)		R476 Q481 Q776 K979 K987 H1097 R1124
Binding residue
(residue number reindexed from 1)		R409 Q414 Q686 K876 K884 H994 R1021
Enzymatic activity
Catalytic site (original residue number in PDB) D837
Catalytic site (residue number reindexed from 1) D747
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2yu9, PDBe:2yu9, PDBj:2yu9
PDBsum2yu9
PubMed17129781
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

[Back to BioLiP]