Structure of PDB 7uwh Chain J

Receptor sequence

>7uwhJ (length=1318) Species: 562 (Escherichia coli)

EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIW
FLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQY
LDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK
KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDL
NDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA
ITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQ
CGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEV
IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQ
MAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR
DCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVA
KTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLK
PTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQ
EQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEK
QVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFRE
GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCG
THEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLH
EQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAI
GVIAAQSIGEPGTQLTMRSSIQVKNKGSIKLSNVKSVVNSSGKLVITSRN
TELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVIT
EVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALK
IVAQYFLPGKAIVQLEDGVQISSGDTLARIPQITGGLPRVADLFEARRPK
EPAILAEISGIVSFGKETKGKRRLVITPDPYEEMIPKWRQLNVFEGERVE
RGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEV
IVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRD
LLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGR
LIPAGTGYAYHQDRMRRR

3D structure

• PDB: 7uwh RNA polymerase drives ribonucleotide excision DNA repair in E. coli.
• Chain: J
• Resolution: 3.1 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	J	R133 N274 R275 R278 R1148 K1170 K1311	R118 N259 R260 R263 R1097 K1119 K1256
BS02	dna	J	S319 R339 R346 R352 P427 T790 G794 Y795 T1068 A1069 G1070 Q1326	S304 R324 R331 R337 P412 T775 G779 Y780 T1039 A1040 G1041 Q1271
BS03	rna	J	R322 R425 D462 D464	R307 R410 D447 D449
BS04	ZN	J	C70 C72 C85	C55 C57 C70
BS05	ZN	J	C814 C888 C895 C898	C799 C873 C880 C883
BS06	MG	J	D460 D462 D464	D445 D447 D449

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

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:7uwh, PDBe:7uwh, PDBj:7uwh
• PDBsum: 7uwh
• PubMed: 37196657
• UniProt: P0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)