Structure of PDB 8pdy Chain J

Receptor sequence

>8pdyJ (length=1355) Species: 562 (Escherichia coli)

KTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIF
GPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTA
HIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTE
EQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSET
KRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFAT
SDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRR
GRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLR
LHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDIL
DEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFD
GDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYY
MTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGE
LVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRIL
GLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVA
EIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQ
EEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITAN
FREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED
DCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNT
LLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKG
EAIGVIAAQSIGEPGTQLTMRTFHAAAESSIQVKNKGSIKLSNVKSVVNS
SGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVAN
WDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTA
GGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGD
TLARIPQESKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGK
RRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILR
LRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSS
DFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISA
ASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRR
RAAGE

3D structure

• PDB: 8pdy Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.
• Chain: J
• Resolution: 2.8 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	P254 R322 R425	P242 R310 R413
BS02	dna	J	R133 R314 K321 R1148 K1170 K1311	R121 R302 K309 R1126 K1148 K1289
BS03	dna	J	S210 E211 T212 L255 F260 T262 K334 R346 T790 A791 G794 Q1326 E1327 R1330	S198 E199 T200 L243 F248 T250 K322 R334 T778 A779 G782 Q1304 E1305 R1308
BS04	ZN	J	C72 C85	C60 C73
BS05	ZN	J	C814 C888 C895 C898	C802 C876 C883 C886
BS06	MG	J	D460 D462 D464	D448 D450 D452

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