Structure of PDB 8sy6 Chain I

Receptor sequence
>8sy6I (length=1135) Species: 562 (Escherichia coli) [Search protein sequence]
MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLE
AAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKL
RLVEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTH
SSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNY
TTEQILDLFFEFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEP
PTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDI
IDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAV
KERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEIT
HKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSL
SVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDE
EGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDD
ANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQ
YVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGE
PVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQE
DRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGA
EVTGGDILVGLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAK
KDLSEELQILEAGLLKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAV
KRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSR
MNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVR
QKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPT
SGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQ
QPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYK
NIVDGNHQMEPGMPESFNVLLKEIRSLGINIELED
3D structure
PDB8sy6 A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.
ChainI
Resolution3.28 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
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 I G1261 K1262 R1269 G1055 K1056 R1063
BS02 rna I Q513 R540 N568 K1073 Q388 R415 N443 K867
BS03 UTP I R678 R1106 R553 R900
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0016779 nucleotidyltransferase activity
GO:0032549 ribonucleoside binding
GO:0034062 5'-3' RNA polymerase activity
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8sy6, PDBe:8sy6, PDBj:8sy6
PDBsum8sy6
PubMed38086811
UniProtP0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)

[Back to BioLiP]