Structure of PDB 5ipn Chain D

Receptor sequence

>5ipnD (length=1362) Species: 562 (Escherichia coli)

EEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGP
VKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHI
WFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQ
YLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKR
KKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSD
LNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGR
AITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLH
QCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDE
VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGD
QMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMT
RDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELV
AKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGL
KPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEI
QEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEE
KQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFR
EGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDC
GTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLL
HEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEA
IGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVK
SVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGG
ETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDS
AERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQ
ISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVS
FGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGP
EAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKA
TIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASL
ATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYA
YHQDRMRRRAAG

3D structure

• PDB: 5ipn Structures of E. coli sigma S-transcription initiation complexes provide new insights into polymerase mechanism.
• Chain: D
• Resolution: 4.61 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	D	Y46 K321 K1311	Y32 K307 K1297
BS02	dna	D	R259 R311 S319 N320 K334 R339 R346 R352 P427 A791 G794 Y795 E1327 R1330	R245 R297 S305 N306 K320 R325 R332 R338 P413 A777 G780 Y781 E1313 R1316
BS03	rna	D	R425 A426 P427 N458 D460 D462 D464 M932	R411 A412 P413 N444 D446 D448 D450 M918
BS04	ZN	D	C70 C85 C88	C56 C71 C74
BS05	ZN	D	C814 C888 C898	C800 C874 C884
BS06	MG	D	D460 D462 D464	D446 D448 D450

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:5ipn, PDBe:5ipn, PDBj:5ipn
• PDBsum: 5ipn
• PubMed: 27035955
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)