Structure of PDB 3po2 Chain B

Receptor sequence

>3po2B (length=1121) Species: 4932 (Saccharomyces cerevisiae)

DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVFI
GRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR
TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPC
VEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQL
EGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLF
KTLFKKLTKDIFRYMQRTVELAINAKTITSGLKYALATGNWGEQKKAMSS
RAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPA
ETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSP
DATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELK
IFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDEYTWSSL
LNEGLVEYIDAEEEESILIAMQPEDLEPAEADVDPAKRIRVSHHATTFTH
CEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMD
TMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMI
MNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTY
DKLDDDGLIAPGVRVSGEDVIIGKTTPISSKRDASTPLRSTENGIVDQVL
VTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTA
EGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVE
GISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKI
HARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLME
ASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLL
FQELMAMNITPRLYTDRSRDF

3D structure

• PDB: 3po2 Structural basis of RNA polymerase II backtracking, arrest and reactivation.
• Chain: B
• Resolution: 3.3 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): D837
• Catalytic site (residue number reindexed from 1): D747
• 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	D399 D505 K507 K510 P511	D332 D430 K432 K435 P436
BS02	rna	B	E529 Y769 K987	E454 Y679 K884
BS03	dna	B	P233 M792 R1122	P166 M702 R1019
BS04	ZN	B	C1163 C1166 C1182 C1185	C1060 C1063 C1079 C1082

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

External links

• PDB: RCSB:3po2, PDBe:3po2, PDBj:3po2
• PDBsum: 3po2
• PubMed: 21346759
• UniProt: P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)