Structure of PDB 8eh9 Chain I

Receptor sequence

>8eh9I (length=1316) Species: 562 (Escherichia coli)

VYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEA
AFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLR
LVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHR
SPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRR
RKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETA
SFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDY
IDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETL
RVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVG
RMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNR
RIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAA
VKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVH
PTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTD
EIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVD
YMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVG
TGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIY
NLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMR
VAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEIT
ADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKDSSLRVPNGVS
GTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRI
RAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEF
EKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGV
ISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIG
DKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAEN
LRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPV
TVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEV
WALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNV
LLKEIRSLGINIELED

3D structure

• PDB: 8eh9 An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options.
• Chain: I
• Resolution: 3.9 Å

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	R151 K163 W183 D199 R200 R542	R150 K162 W182 D198 R199 R541
BS02	dna	I	N139 R143 K496 F514 G1261 K1262 R1269	N138 R142 K495 F513 G1236 K1237 R1244
BS03	rna	I	Q510 Q513 R540 P564 N568 R687 Q688 K1073 H1237	Q509 Q512 R539 P563 N567 R686 Q687 K1048 H1212
BS04	1N7	I	Q46 Y47 Y179 S398 A399 Y584	Q45 Y46 Y178 S397 A398 Y583

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

External links

• PDB: RCSB:8eh9, PDBe:8eh9, PDBj:8eh9
• PDBsum: 8eh9
• PubMed: 36795753
• UniProt: P0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)