Structure of PDB 1r9s Chain B Binding Site BS03

Receptor Information

>1r9s Chain B (length=1097) Species: 4932 (Saccharomyces cerevisiae)

DESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTL
IISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKKVFI
GRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQER
SAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSAR
TIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPC
VEDGFVIQDRETALDFIGKEKRIQYAKDILQKEFLPHITQLEGFESRKAF
FLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTK
DIFRYMQRTVELAINAKTITSGLKYALATGNWGAGVSQVLNRYTYSSTLS
HLRRTNTPIAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGT
DPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMET
LRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHK
ELKVRKGHIAKLMATEYQDEYTWSSLLNEGLVEYIDAEEEESILIAMQPE
DLEPAEADVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQS
PRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKF
RELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEK
KYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGK
TTPISSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIG
DKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLI
ECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHT
GKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGG
LRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNH
NQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF

Ligand information

• Ligand ID: UTP
• InChI: InChI=1S/C9H15N2O15P3/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: PGAVKCOVUIYSFO-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
  CACTVS 3.341: O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P@](O)(=O)O[P@](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
• Formula: C9 H15 N2 O15 P3
• Name: URIDINE 5'-TRIPHOSPHATE
• ChEMBL: CHEMBL336296
• DrugBank: DB04005
• ZINC: ZINC000003861755
• PDB chain: 1r9s Chain R Residue 3000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1r9s Structural basis of transcription: nucleotide selection by rotation in the RNA polymerase II active center.
• Resolution: 4.25 Å
• Binding residue (original residue number in PDB): R766 Y769 K987 R1020
• Binding residue (residue number reindexed from 1): R652 Y655 K860 R893
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): D837
• Catalytic site (residue number reindexed from 1): D723
• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

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:1r9s, PDBe:1r9s, PDBj:1r9s
• PDBsum: 1r9s
• PubMed: 15537538
• UniProt: P08518|RPB2_YEAST DNA-directed RNA polymerase II subunit RPB2 (Gene Name=RPB2)