Structure of PDB 7xyb Chain D

Receptor sequence

>7xybD (length=1338) Species: 287 (Pseudomonas aeruginosa)

EFDAIRIGLASPEMIRSWSFGEVKKPETINYRTFKPERDGLFCAKIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVALAKVRRERMGHIELASPVAHIW
FLKSLPSRIGLLLDMTLRDIERVLYFESYVVIDPGMTTLEKGQLLNDEQY
FEALEEFGDDFDARMGAEAVHELLNAIDLEHEIGRLREEIPQTNSETKIK
KLSKRLKLMEAFQGSGNKPEWMVLTVLPVLPPDLRPLVPLDGGRFATSDL
NDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRA
ITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPTLRLHQ
CGLPKKMALELFKPFIFGKLEGRGMATTIKAAKKMVERELPEVWDVLAEV
IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQ
MAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVMGLYYMTR
EAINAKGEGMAFADLQEVDRAYRSGQASLHARVKVRINEKIKGEDGQLTA
NTRIVDTTVGRALLFQVVPAGLPFDVVNQSMKKKAISKLINHCYRVVGLK
DTVIFADQLMYTGFAYSTISGVSIGVNDFVIPDEKARIINAATDEVKEIE
SQYASGLVTQGEKYNKVIDLWSKANDEVSKAMMANLSKEKVVDREGKEVD
QESFNSMYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFRE
GLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEIDCG
TEHGLLMSPHIEGGDVVEPLGERVLGRVIARDVFKPGSDEVIVPAGTLID
EKWVDFLEVMSVDEVVVRSPITCETRHGICAMCYGRDLARGHRVNIGEAV
GVIAAQSIGEPGTQLTADNVQVKNGGTIRLHNLKHVVRADGALVAVSRSG
ELAVADDFGRERERYKLPYGAVISVKEGDKVDPGAIVAKWDPHTHPIVTE
VDGTVAFVGMEEGITVKRQTDELTGLTNIEVMDPKDRPAAGKDIRPAVKL
IDAAGKDLLLPGTDVPAQYFLPANALVNLTDGAKVSIGDVVARIPQTGGL
PRVADLFEARRPKEPSILAEISGTISFGKETKGKRRLVITPNDGSDPYEE
LIPKWRHLNVFEGEQVNRGEVISDGPSNPHDILRLLGVSSLAKYIVNEIQ
DVYRLQGVKINDKHIETILRQMLRKVEVSESGDSSFIKGDQVELTQVLEE
NEQLGTEDKFPAKYERVLLGITKASLSTESFISAASFQETTRVLTEAAVT
GKRDFLRGLKENVVVGRLIPAGTGLAYHSERKRQRDLG

3D structure

• PDB: 7xyb Structural basis of AlpA-dependent transcription antitermination.
• Chain: D
• Resolution: 3.7 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	D	R425 D462 D464	R410 D447 D449
BS02	dna	D	R270 R278 R1148	R255 R263 R1110
BS03	dna	D	S210 E211 R311 G318 S319 R346 R352 A791 Y795 Q1326 E1327	S195 E196 R296 G303 S304 R331 R337 A776 Y780 Q1288 E1289
BS04	MG	D	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: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

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex

External links

• PDB: RCSB:7xyb, PDBe:7xyb, PDBj:7xyb
• PDBsum: 7xyb
• PubMed: 35871295
• UniProt: Q9HWC9|RPOC_PSEAE DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)