Structure of PDB 2yu9 Chain B

Receptor sequence
>2yu9B (length=1121) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTY
EAIDKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSE
KVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLY
GREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQ
MLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKE
FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLA
GPLLAQLFKTLFKKLTKDIFRYMQRTVELAINAKTITSGLKYALATGNWG
EQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVC
PAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQ
SPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKE
LKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWS
SLLNEGLVEYIDAEEEESILIAMQPEDLEPADVDPAKRIRVSHHATTFTH
CEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMD
TMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMI
MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTY
DKLDDDGLIAPGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVL
VTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTA
EGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVE
GISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKI
HARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLME
ASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLL
FQELMAMNITPRLYTDRSRDF
3D structure
PDB2yu9 Structural Basis of Transcription: Role of the Trigger Loop in Substrate Specificity and Catalysis
ChainB
Resolution3.4 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) D747
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 R476 Q481 Q776 K979 K987 H1097 R1124 R409 Q414 Q686 K876 K884 H994 R1021
BS02 dna B A462 T791 R857 R1122 L1128 R1129 A395 T701 R767 R1019 L1025 R1026
BS03 UTP B R766 K987 S1019 R676 K884 S916
BS04 ZN B C1163 C1166 C1182 C1185 C1060 C1063 C1079 C1082
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:2yu9, PDBe:2yu9, PDBj:2yu9
PDBsum2yu9
PubMed17129781
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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