Structure of PDB 7mko Chain D

Receptor sequence

>7mkoD (length=1344) Species: 83333 (Escherichia coli K-12)

TEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFG
PVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAH
IWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEE
QYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETK
RKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATS
DLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG
RAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRL
HQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILD
EVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDG
DQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYM
TRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGEL
VAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILG
LKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAE
IQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQE
EKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANF
REGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDD
CGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTL
LHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGE
AIGVIAAQSIGEPGTQLTMRTFAESSIQVKNKGSIKLSNVKSVVNSSGKL
VITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPH
TMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKD
LRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLAR
IPTGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDG
SDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRY
IVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEY
SRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVL
TEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAG

3D structure

• PDB: 7mko Structural basis of RNA polymerase recycling by the Swi2/Snf2 family of ATPase RapA in Escherichia coli.
• Chain: D
• Resolution: 3.15 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	L120 K321 R1148	L107 K308 R1116
BS02	rna	D	V253 L255 D462 D464	V240 L242 D449 D451
BS03	dna	D	S210 E211 K213 R259 R311 S319 K334 R339 R346 R352 T790 A791 G794 Y795 Q1326 E1327 R1330	S197 E198 K200 R246 R298 S306 K321 R326 R333 R339 T777 A778 G781 Y782 Q1294 E1295 R1298
BS04	MG	D	D460 D462 D464	D447 D449 D451
BS05	ZN	D	C70 C72 C85	C57 C59 C72
BS06	ZN	D	C814 C888 C895 C898	C801 C875 C882 C885
BS07	2TM	D	R425 N458 R731 M932 R933	R412 N445 R718 M919 R920

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:7mko, PDBe:7mko, PDBj:7mko
• PDBsum: 7mko
• PubMed: 34774797
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)