Structure of PDB 3hoy Chain B

Receptor sequence
>3hoyB (length=1105) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRKVF
IGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQE
RSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSA
RTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKP
CVEDGFVIQDRETALDFIGRKEKRIQYAKDILQKEFLPHITQLEGFESRK
AFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKL
TKDIFRYMQRTVELAINAKTITSGLKYALATGNWGAGVSQVLNRYTYSST
LSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSL
MSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHR
NPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVE
DDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEES
ILIAMQPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHPSMILGVAASII
PFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTT
RAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFF
RSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVS
GEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVR
TTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPS
RMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGF
EVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPV
EGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLM
TVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTD
RSRDF
3D structure
PDB3hoy Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
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) D731
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 R504 D505 M792 R857 R942 R1122 R1129 M1133 R413 D414 M686 R751 R823 R1003 R1010 M1014
BS02 rna B Q776 K979 K987 H1097 Q1112 Q670 K860 K868 H978 Q993
BS03 ZN B C1163 C1185 C1044 C1066
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:3hoy, PDBe:3hoy, PDBj:3hoy
PDBsum3hoy
PubMed19560423
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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