Structure of PDB 6p19 Chain D

Receptor sequence

>6p19D (length=1327) Species: 83333 (Escherichia coli K-12)

EEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGP
VKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHI
WFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQ
YLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKR
KKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSD
LNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGR
AITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLH
QCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDE
VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGD
QMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMT
RDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELV
AKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGL
KPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEI
QEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEE
KQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFR
EGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDC
GTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLL
HEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEA
IGVIAAQSIGEPGTQLSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGR
TKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM
IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLI
PGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQGGLPRVADLFEARR
PKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVF
EGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKIN
DKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVG
ATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKE
NVIVGRLIPAGTGYAYHQDRMRRRAAG

3D structure

• PDB: 6p19 Structural basis of Q-dependent antitermination.
• Chain: D
• Resolution: 3.8 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	dna	D	Y46 R47 R1148	Y32 R33 R1099
BS02	dna	D	S210 K213 L255 R270 R311 S319 R339 R346 R352 A426 P427 R798 Q1326	S196 K199 L241 R256 R297 S305 R325 R332 R338 A412 P413 R784 Q1277
BS03	rna	D	K76 R77 V253 R322 D464	K62 R63 V239 R308 D450
BS04	ZN	D	C70 L71 C72	C56 L57 C58
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:6p19, PDBe:6p19, PDBj:6p19
• PDBsum: 6p19
• PubMed: 31455742
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)