Structure of PDB 5ui8 Chain J Binding Site BS01

Receptor Information

>5ui8 Chain J (length=1336) Species: 83334 (Escherichia coli O157:H7)

MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFK
PERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRE
RMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGG
MTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQ
LREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLR
PLVFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDAL
LDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVIT
VGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEA
VVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAA
YNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDV
VLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYE
KDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLN
TCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISE
AEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETV
INRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIE
TPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQD
LVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADI
LVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARG
HIINKGEAIGVIAAQSIGEPGTQLTSSIQVKNKGSIKLSNVKSVVNSSGK
LVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDP
HTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGK
DLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLA
RIPQTGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPV
DGSDPYEEMIPKWRGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNE
VQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVK
IANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAA
VAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRR

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 5ui8 Chain J Residue 1501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5ui8 Crystal structure of Aquifex aeolicus sigma (N) bound to promoter DNA and the structure of sigma (N)-holoenzyme.
• Resolution: 3.76 Å
• Binding residue (original residue number in PDB): D460 D462
• Binding residue (residue number reindexed from 1): D454 D456
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA polymerase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0006352 DNA-templated transcription initiation
• GO:0006879 intracellular iron ion homeostasis
• GO:0009408 response to heat
• GO:0031564 transcription antitermination
• GO:0032784 regulation of DNA-templated transcription elongation
• GO:0036460 cellular response to cell envelope stress
• GO:0042128 nitrate assimilation
• GO:0044780 bacterial-type flagellum assembly
• GO:0046677 response to antibiotic
• GO:0048870 cell motility
• GO:0071973 bacterial-type flagellum-dependent cell motility
• GO:0090605 submerged biofilm formation
• GO:2000142 regulation of DNA-templated transcription initiation

Cellular Component

• GO:0000345 cytosolic DNA-directed RNA polymerase complex
• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005737 cytoplasm
• GO:0005829 cytosol
• GO:0008023 transcription elongation factor complex
• GO:0016020 membrane

External links

• PDB: RCSB:5ui8, PDBe:5ui8, PDBj:5ui8
• PDBsum: 5ui8
• PubMed: 28223493
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)