Structure of PDB 8pim Chain J

Receptor sequence

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

EEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGP
VKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHI
WFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQ
YLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKR
KKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSD
LNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGR
AITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLH
QCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDE
VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGD
QMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMT
RDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELV
AKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGL
KPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEI
QEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEE
KQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFR
EGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDC
GTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLL
HEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEA
IGVIAAQSIGEPGTQLTMRTFESSIQVKNKGSIKLSNVKSVVNSSGKLVI
TSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTM
PVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLR
PALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIP
QITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDG
SDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRY
IVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEY
SRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVL
TEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAA

3D structure

• PDB: 8pim Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.
• Chain: J
• Resolution: 3.4 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	R322 K398 R425 P427 D460 D462 D464	R308 K384 R411 P413 D446 D448 D450
BS02	dna	J	R47 R133 R270 R271 N274 R314 R1148 K1167 T1169 K1311	R33 R119 R256 R257 N260 R300 R1116 K1135 T1137 K1279
BS03	dna	J	S210 L255 R259 R270 R311 S319 K334 R339 R346 R352 T790 A791 Q1326	S196 L241 R245 R256 R297 S305 K320 R325 R332 R338 T776 A777 Q1294
BS04	ZN	J	C72 C85	C58 C71
BS05	ZN	J	C888 C895 C898	C874 C881 C884
BS06	MG	J	D460 D462	D446 D448

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