Structure of PDB 7ubn Chain C

Receptor sequence

>7ubnC (length=1339) Species: 562 (Escherichia coli)

SYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAF
RSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLV
IYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSP
GVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRK
LPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASF
DIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYID
ESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRV
DPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRM
KFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRI
RSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVK
EFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPT
HYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEI
HYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYM
DVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTG
MERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNL
TKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVA
FMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITAD
IPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLR
AIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQL
KQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLT
DEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVY
LAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGV
PSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGA
DVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGD
LPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSL
VTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTK
MYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE

3D structure

• PDB: 7ubn In transcription antitermination by Q lambda , NusA induces refolding of Q lambda to form a nozzle that extends the RNA polymerase RNA-exit channel.
• Chain: C
• Resolution: 3.36 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	C	R151 R175 W183 D199 R200 R371 I445 R473 L538 T539 R542 E546	R148 R172 W180 D196 R197 R368 I442 R470 L535 T536 R539 E543
BS02	dna	C	N139 G1261 K1262 R1269 M1273	N136 G1258 K1259 R1266 M1270
BS03	rna	C	R540 Q688 K1065 K1073 H1237 Y1251 S1252 L1253	R537 Q685 K1062 K1070 H1234 Y1248 S1249 L1250

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:7ubn, PDBe:7ubn, PDBj:7ubn
• PDBsum: 7ubn
• PubMed: 35951650
• UniProt: P0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)