Structure of PDB 4bbs Chain B

Receptor sequence
>4bbsB (length=1150) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARL
RNLTYSSGLFVDVKKRTYEAIDELKYELGKVFIGRLPIMLRSKNCYLSEA
TESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPI
SHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVI
IFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFI
GRRGKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCAL
DRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAH
DFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSS
TLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCIS
VGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARL
METLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESL
GHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESILIAM
QPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDH
NQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEY
LKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMD
QEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVI
IGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIP
QIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVA
HLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYN
GHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSR
DGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAK
LNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF
3D structure
PDB4bbs Structure and Function of the Initially Transcribing RNA Polymerase II-TFIIB Complex
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) D776
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 Q776 K979 Q441 Q715 K905
BS02 dna B M792 R857 R942 R1122 R1129 M731 R796 R868 R1048 R1055
BS03 ZN B C1163 C1185 C1089 C1111
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
View graph for
Cellular Component
External links
PDB RCSB:4bbs, PDBe:4bbs, PDBj:4bbs
PDBsum4bbs
PubMed23151482
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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