Structure of PDB 8pid Chain J

Receptor sequence

>8pidJ (length=1343) Species: 562 (Escherichia coli)

EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIW
FLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQY
LDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK
KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDL
NDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA
ITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQ
CGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEV
IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQ
MAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR
DCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVA
KTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLK
PTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQ
EQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEK
QVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFRE
GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCG
THEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLH
EQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAI
GVIAAQSIGEPGTQLTMRTFHESSIQVKNKGSIKLSNVKSVVNSSGKLVI
TSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTM
PVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLR
PALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIP
QITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDG
SDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRY
IVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEY
SRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVL
TEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAA

3D structure

• PDB: 8pid Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.
• Chain: J
• Resolution: 3.0 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 R270 R271 R314 R1148 K1170 K1311	R32 R118 R255 R256 R299 R1116 K1138 K1279
BS02	dna	J	S210 L255 S319 K334 R339 R346 T790 A791 Q1326 E1327	S195 L240 S304 K319 R324 R331 T775 A776 Q1294 E1295
BS03	rna	J	V253 L255 R425 P427 N458 D460 D462 D464 R731 Q929	V238 L240 R410 P412 N443 D445 D447 D449 R716 Q914
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:8pid, PDBe:8pid, PDBj:8pid
• PDBsum: 8pid
• PubMed: 38589445
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)