Structure of PDB 4yln Chain P

Receptor sequence

>4ylnP (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: 4yln Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble.
• Chain: P
• Resolution: 5.5 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	P	Y46 R47 K321 R1148	Y32 R33 K307 R1134
BS02	dna	P	R311 K334 R346 R352 A426 T790 A791 Y795 Q1326 E1327 R1330	R297 K320 R332 R338 A412 T776 A777 Y781 Q1312 E1313 R1316
BS03	rna	P	R425 P427 N458 D464 M932	R411 P413 N444 D450 M918
BS04	ZN	P	C70 C85 C88	C56 C71 C74
BS05	ZN	P	C814 R883 C895	C800 R869 C881
BS06	MG	P	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: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

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex

External links

• PDB: RCSB:4yln, PDBe:4yln, PDBj:4yln
• PDBsum: 4yln
• PubMed: 25866247
• UniProt: A7ZUK2|RPOC_ECO24 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)