Structure of PDB 8jch Chain B

Receptor sequence

>8jchB (length=1157) Species: 559292 (Saccharomyces cerevisiae S288C)

FEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDS
TLILESRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLF
VDVKKRTYGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFI
INGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTL
QVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYD
VNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKD
ILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKK
RLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTIT
SGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGK
LAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITF
LSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKG
DINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGH
IAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQP
EDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIP
FPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTR
AMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFR
SYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSG
EDVIIGKTTPISAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVR
VRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAI
PSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSR
GFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQ
PVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICG
LMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLY
TDRSRDF

3D structure

• PDB: 8jch Structural basis of exoribonuclease-mediated mRNA transcription termination
• Chain: B
• Resolution: 2.7 Å

Enzymatic activity

• 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	R249 I251 Y275 R398 D399 K404 I502 K507 L508	R195 I197 Y221 R344 D345 K350 I448 K450 L451
BS02	rna	B	A477 Q481 Q776 R884 A930 Y931 K979 K987	A423 Q427 Q719 R827 A863 Y864 K912 K920
BS03	dna	B	R857 R942 G1121 R1122 R1129 M1133	R800 R875 G1054 R1055 R1062 M1066
BS04	ZN	B	C1163 C1166	C1096 C1099

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:8jch, PDBe:8jch, PDBj:8jch
• PDBsum: 8jch
• PubMed: 38538796
• UniProt: P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)