Structure of PDB 3gtm Chain B

Receptor sequence
>3gtmB (length=1104) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence]
DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVFI
GRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR
TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPC
VEDGFVIQDRETALDFIGKEKRIQYAKDILQKEFLPHITQLEGFESRKAF
FLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTK
DIFRYMQRTVELAINAKTITSGLKYALATGNWGEQSSRAGVSQVLNRYTY
SSTLSHLRRTNTPIKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLM
SCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRN
PARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVED
DESLGHKELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESI
LIAMQPEDLEPAEADVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIP
FPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTR
AMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFR
SYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSG
EDVIIGKTTPISSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRT
TKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSR
MTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFE
VMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVE
GRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMT
VIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDR
SRDF
3D structure
PDB3gtm 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) D730
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 K987 H1097 R1124 Q393 Q669 K859 K867 H977 R1004
BS02 dna B M792 R857 R942 G1121 S1123 L1128 R1129 M1133 M685 R750 R822 G1001 S1003 L1008 R1009 M1013
BS03 ZN B C1163 C1185 C1043 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
View graph for
Cellular Component
External links
PDB RCSB:3gtm, PDBe:3gtm, PDBj:3gtm
PDBsum3gtm
PubMed19478184
UniProtP08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)

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