Structure of PDB 3s15 Chain B

Receptor sequence
>3s15B (length=1114) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTY
EAIDKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSE
KVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLY
GREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQ
MLEMLKPCVEDGFVIQDRETALDFIGKEKRIQYAKDILQKEFLPHITQLE
GFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFK
TLFKKLTKDIFRYMQRTVELAINAKTITSGLKYALATGNWGEQKKAMSSR
AGVSQVLNRYTYSSTLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQA
CGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFV
NGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGR
VYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVE
YIDAEEEESILIAMQPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHPSM
ILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILY
YPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSID
RGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDG
LIAPGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQDG
LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDL
IINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLR
EHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGP
MQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRV
HICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAM
NITPRLYTDRSRDF
3D structure
PDB3s15 Initiation complex structure and promoter proofreading.
ChainB
Resolution3.3 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) D740
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 Q776 K979 K987 H1097 R400 Q679 K869 K877 H987
BS02 dna B A462 T791 M792 R857 R942 R1129 A386 T694 M695 R760 R832 R1019
BS03 ZN B C1163 C1166 C1185 C1053 C1056 C1075
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
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3s15, PDBe:3s15, PDBj:3s15
PDBsum3s15
PubMed21798951
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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