Structure of PDB 8pfg Chain J

Receptor sequence

>8pfgJ (length=1317) Species: 562 (Escherichia coli)

EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLY
FESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLK
SMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILT
VLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDI
IVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQ
NLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGL
ATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPV
LIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNI
LSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSG
LASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYS
IVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVG
IDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAAN
DRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQL
AGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKT
ANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVL
GRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDT
DFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFESSIQ
VKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGA
VLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTD
ELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFL
PGKAIVQLEDGVQISSGDTLARIPQITGGLPRVADLFEARRPKEPAILAE
ISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGD
VISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVR
QMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLG
ITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIP
AGTGYAYHQDRMRRRAA

3D structure

• PDB: 8pfg 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	rna	J	V253 L255 R322 R425 P427 D460 D462 D464	V213 L215 R282 R385 P387 D420 D422 D424
BS02	dna	J	S210 K213 L255 T262 R270 R311 S319 K334 R339 R346 T790 A791 Q1326	S170 K173 L215 T222 R230 R271 S279 K294 R299 R306 T750 A751 Q1268
BS03	dna	J	R133 R271 R278 R314 R1148 K1170	R93 R231 R238 R274 R1090 K1112
BS04	ZN	J	C895 C898	C855 C858
BS05	MG	J	D460 D462 D464	D420 D422 D424

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