Structure of PDB 7dy6 Chain D

Receptor sequence
>7dy6D (length=1355) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
KDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKP
ERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRER
MGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGM
TNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQL
REELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRP
LVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQE
AVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNKRVDYSGRSV
ITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVERE
EAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVC
AAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQ
DVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITE
YEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKM
LNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEII
SEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTE
TVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSI
IETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVA
QDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTA
DILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLA
RGHIINKGEAIGVIAAQSIGEPGTQLTMAAAESSIQVKNKGSIKLSNVKS
VVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGE
TVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSA
ERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQI
SSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSF
GKETKGKRRLVITPVPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHD
ILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNA
GSSDFLEGEQVEYSRVKIANRELEANGKATYSRDLLGITKASLATESFIS
AASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMR
RRAAG
3D structure
PDB7dy6 A unique binding between SspA and RNAP beta' NTH across low-GC Gram-negative bacteria facilitates SspA-mediated transcription regulation.
ChainD
Resolution3.68 Å
3D
structure
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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 R1148 K1167 K1170 K1311 R1133 K1152 K1155 K1290
BS02 dna D L120 Y795 E1327 L119 Y791 E1306
BS03 MG D D460 D464 D456 D460
BS04 ZN D C72 C85 C71 C84
BS05 ZN D C814 C888 C895 C898 C810 C884 C891 C894
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7dy6, PDBe:7dy6, PDBj:7dy6
PDBsum7dy6
PubMed34735884
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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