Structure of PDB 3gtk Chain B

Receptor sequence
>3gtkB (length=1153) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
ILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARL
RNLTYSSGLFVDVKKKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFD
MGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGS
RFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEIL
EHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKR
IQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDR
DHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAI
NAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRT
NTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPI
ITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLR
RKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVR
KGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIA
MQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAAS
IIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLG
TTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSL
FFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVR
VSGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVR
VRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAI
PSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSR
GFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQ
PVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICG
LMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLY
TDR
3D structure
PDB3gtk Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.
ChainB
Resolution3.8 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) D783
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 K471 Q481 E529 G530 Y769 Q776 K979 K987 S1019 R1020 K423 Q433 E475 G476 Y715 Q722 K912 K920 S952 R953
BS02 dna B K210 M792 G1121 R1122 R1129 K162 M738 G1054 R1055 R1062
BS03 ZN B C1163 C1185 C1096 C1118
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:3gtk, PDBe:3gtk, PDBj:3gtk
PDBsum3gtk
PubMed19478184
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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