Structure of PDB 8pim Chain I

Receptor sequence

>8pimI (length=1321) Species: 562 (Escherichia coli)

MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLE
AAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKL
RLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLH
RSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDR
RRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGET
ASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKD
YIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISET
LRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAV
GRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGN
RRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISA
AVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDV
HPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVT
DEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQV
DYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLV
GTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDI
YNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNM
RVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEI
TADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKDVKDSSLRVP
NGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGL
FSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDEL
KHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHG
NKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAA
KGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMR
LAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQF
ERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFG
EMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPE
SFNVLLKEIRSLGINIELEDE

3D structure

• PDB: 8pim Concerted transformation of a hyper-paused transcription complex and its reinforcing protein.
• Chain: I
• Resolution: 3.4 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	rna	I	Q510 Q513 R540 P564 N568 Q688 K1065 K1073 S1250 Y1251 R1301 T1302 Y1305	Q510 Q513 R540 P564 N568 Q688 K1044 K1052 S1229 Y1230 R1280 T1281 Y1284
BS02	dna	I	Y62 R151 W183 D199 R200 R201 R371 I445 R473 L538 R542 V547	Y62 R151 W183 D199 R200 R201 R371 I445 R473 L538 R542 V547
BS03	dna	I	K203 F514 R542 G1261 K1262 R1269	K203 F514 R542 G1240 K1241 R1248

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:8pim, PDBe:8pim, PDBj:8pim
• PDBsum: 8pim
• PubMed: 38589445
• UniProt: P0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)