Structure of PDB 8pen Chain J

Receptor sequence

>8penJ (length=1342) Species: 562 (Escherichia coli)

EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIW
FLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQY
LDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK
KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDL
NDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA
ITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQ
CGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEV
IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQ
MAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR
DCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVA
KTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLK
PTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQ
EQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEK
QVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFRE
GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCG
THEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLH
EQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAI
GVIAAQSIGEPGTQLTMRTFESSIQVKNKGSIKLSNVKSVVNSSGKLVIT
SRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMP
VITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRP
ALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQ
ITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGS
DPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYI
VNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYS
RVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLT
EAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAA

3D structure

• PDB: 8pen Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.
• Chain: J
• Resolution: 3.1 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	J	R47 R133 R271 R314 R1148 K1167 K1170 K1311	R32 R118 R256 R299 R1115 K1134 K1137 K1278
BS02	dna	J	S210 E211 L255 R259 K334 R346 T790 A791 Q1326	S195 E196 L240 R244 K319 R331 T775 A776 Q1293
BS03	rna	J	V253 L255 D460 D462 D464	V238 L240 D445 D447 D449
BS04	ZN	J	C72 C85	C57 C70
BS05	ZN	J	C895 C898	C880 C883
BS06	MG	J	D460 D462	D445 D447

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:8pen, PDBe:8pen, PDBj:8pen
• PDBsum: 8pen
• PubMed: 38589445
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)