Structure of PDB 7dy6 Chain D Binding Site BS02

Receptor Information
>7dy6 Chain D (length=1355) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
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
Ligand information
>7dy6 Chain G (length=48) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
ccctgcatccgtgatagacaatttaacacttttgtcaatcattttgtt
Receptor-Ligand Complex Structure
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PDB7dy6 A unique binding between SspA and RNAP beta' NTH across low-GC Gram-negative bacteria facilitates SspA-mediated transcription regulation.
Resolution3.68 Å
Binding residue
(original residue number in PDB)		L120 Y795 E1327
Binding residue
(residue number reindexed from 1)		L119 Y791 E1306
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
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
View graph for
Biological Process
View graph for
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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