Structure of PDB 7yp9 Chain C

Receptor sequence

>7yp9C (length=1230) Species: 83333 (Escherichia coli K-12)

VYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEA
AFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLR
LVIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKT
HSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALN
YTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVE
KGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAAN
MELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALV
EIYRMPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGIL
SKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVR
VERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNP
LSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIG
LINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQAN
SNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPF
LEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKR
GGVVQYVDASRIVIKVNEDEMYAGIDIYNLTKYTRSNQNTCINQMPCVSL
GEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVV
QEDRFTTIHIQELACVSREEITADIPLSKLDESGIVYIGAEVTGGDILVG
KVTPKVKDSSLRVPNGVSGTVIDVQVFTDKRALEIEEMQLKQAKKDLSEE
LQILEAQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRI
QPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIG
QILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVD
LSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQI
RLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLG
GKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVD
GNHQMEPGMPESFNVLLKEIRSLGINIELE

3D structure

• PDB: 7yp9 Structural basis for intrinsic transcription termination.
• Chain: C
• Resolution: 3.58 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	T164 R180 G181 W183 D199 R200 D393 R394 R465 V469 R473 P535 R542	T150 R166 G167 W169 D185 R186 D373 R374 R445 V449 R453 P515 R522
BS02	dna	C	N139 R202 K203 F514 R542 G1261 K1262 Q1268 R1269 M1273	N125 R188 K189 F494 R522 G1151 K1152 Q1158 R1159 M1163
BS03	rna	C	S509 Q510 Q513 L533 R540 P564 P567 I572 R687 Q688 K1065 K1073 H1237 S1250 L1253 L1259	S489 Q490 Q493 L513 R520 P544 P547 I552 R667 Q668 K955 K963 H1127 S1140 L1143 L1149

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:7yp9, PDBe:7yp9, PDBj:7yp9
• PDBsum: 7yp9
• PubMed: 36631609
• UniProt: P0A8V2|RPOB_ECOLI DNA-directed RNA polymerase subunit beta (Gene Name=rpoB)