Structure of PDB 6bqf Chain B

Receptor sequence
>6bqfB (length=1097) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVF
IGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQE
RSAGNIVQVFKKAAPSPISHVAEIRSAISTLQVKLYGREGSSARTIKATL
PYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFV
IQDRETALDFIGRRGKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLG
YMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIF
RYMQRTLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYS
STLSHLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCI
SVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPAR
LMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDES
LGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESILIA
MQPEDLEPDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQ
SPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLK
FRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQE
KKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIG
KTTPITAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKI
PQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTV
AHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMY
NGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRS
RDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIA
KLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDR
3D structure
PDB6bqf Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.
ChainB
Resolution3.35 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) D724
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 T791 R1129 T678 R1006
BS02 rna B R476 A477 Q776 K987 H1097 R387 A388 Q663 K864 H974
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:6bqf, PDBe:6bqf, PDBj:6bqf
PDBsum6bqf
PubMed29487211
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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