Structure of PDB 8reb Chain D

Receptor sequence
>8rebD (length=1330) Species: 83333 (Escherichia coli K-12) [Search protein sequence]
LLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPER
DGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMG
HIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTN
LERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLRE
ELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLV
PLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAV
DALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRS
VITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVER
EEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLV
CAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPS
QDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRIT
EYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISK
MLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEI
ISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQT
ETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGS
IIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDV
AQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGT
ADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDL
ARGHIINKGEAIGVIAAQSIGEPGTQLTMAAESSIQVKNKGSIKLSNVKS
VVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGE
TVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQSSLVVLDSAERRPALK
IVDAQGNDVAQYFLPGKAIVQLEDGVQISSGDTLARIPQGGLPRVADLFE
ARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQL
NVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGV
KINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANG
KVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRG
LKENVIVGRLIPAGTGYAYHQDRMRRRAAG
3D structure
PDB8reb Structural basis of sigma 54 displacement and promoter escape in bacterial transcription.
ChainD
Resolution3.4 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 R133 R281 R1148 K1170 K1172 R130 R278 R1102 K1124 K1126
BS02 rna D R425 D464 R422 D461
BS03 dna D L255 R259 F260 A261 S319 R346 R352 T790 Y795 E1327 L252 R256 F257 A258 S316 R343 R349 T787 Y792 E1281
BS04 MG D D460 D462 D464 D457 D459 D461
BS05 ZN D C814 C888 C895 C898 C811 C885 C892 C895
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:8reb, PDBe:8reb, PDBj:8reb
PDBsum8reb
PubMed38170755
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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