Structure of PDB 8k58 Chain D

Receptor sequence

>8k58D (length=1352) Species: 83333 (Escherichia coli K-12)

TEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFG
PVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAH
IWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEE
QYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETK
RKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATS
DLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRG
RAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRL
HQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILD
EVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDG
DQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYM
TRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGEL
VAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILG
LKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAE
IQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQE
EKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANF
REGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDD
CGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTL
LHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGE
AIGVIAAQSIGEPGTQLTMAAAESSIQVKNKGSIKLSNVKSVVNSSGKLV
ITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHT
MPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDL
RPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARI
PQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRR
LVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLR
GVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDF
LEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAAS
FQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRA
AG

3D structure

• PDB: 8k58 TIEA inhibits Sigma70-dependent transcriptions, accelerates elongation speed and elevates transcription error
• Chain: D
• Resolution: 3.15 Å

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	E42 Y46 R47 L120 R271 N274 R278 R1148 T1169 K1170 G1171	E29 Y33 R34 L107 R258 N261 R265 R1124 T1145 K1146 G1147
BS02	dna	D	K118 L255 R259 A261 D267 R270 R311 T317 N320 K334 Q335 L342 R346 T790 A791 G794 Y795 K1172 M1189 W1193 E1327	K105 L242 R246 A248 D254 R257 R298 T304 N307 K321 Q322 L329 R333 T777 A778 G781 Y782 K1148 M1165 W1169 E1303
BS03	rna	D	V253 R425	V240 R412

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:8k58, PDBe:8k58, PDBj:8k58
• PDBsum: 8k58
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)