Structure of PDB 5ot2 Chain B

Receptor sequence
>5ot2B (length=1104) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVFI
GRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSALEKGSISTLQVKLYGREGSSARTI
KATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVE
DGFVIQDRETALDFIGRKEKRIQYAKDILQKEFLPHITQLEGFESRKAFF
LGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKD
IFRYMQRTVLAINAKTITSGLKYALATGNWGEQAMSSRAGVSQVLNRYTY
SSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKN
LSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHG
VHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLF
IVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEE
EESILIAMQPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHPSMILGVAA
SIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPL
GTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRS
LFFRSYMDQEKKYGMSITETFEKPQRTRMKHGTYDKLDDDGLIAPGVRVS
GEDVIIGKTTPISKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRT
TKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSR
MTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFE
VMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVE
GRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMT
VIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDR
SRDF
3D structure
PDB5ot2 Mechanism of RNA polymerase II stalling by DNA alkylation.
ChainB
Resolution3.2 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) D734
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 M792 R942 G1121 R1122 R1129 T688 M689 R822 G1001 R1002 R1009
BS02 rna B Q481 Q776 K979 K987 R1124 Q393 Q673 K859 K867 R1004
BS03 ZN B C1163 C1166 C1182 C1185 C1043 C1046 C1062 C1065
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:5ot2, PDBe:5ot2, PDBj:5ot2
PDBsum5ot2
PubMed29087308
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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