Structure of PDB 6j9e Chain D

Receptor sequence

>6j9eD (length=1200) Species: 360094 (Xanthomonas oryzae pv. oryzae PXO99A)

MKDLLNLFNQQRQTLDFDAIKIALASPDLIRSWSYGEVKKPETINYRTFK
PERDGLFCAAIFGPIKDYECLCGKYKRMKHRGVVCEKCGTEVTLAKVRRE
RMGHIDLASPVAHIWFLKSLPSRIGLMLDMTLRDIERVLYFEAYVVTRRQ
LLTEEQYLTARQEYNDDFDAAMGAEAVYELLRTIDLQSEMTRLREEIAST
GSETKLKRLTKRIKLIEAFLESGNRPEWMVMTVLPVLPPDLRPLVPLDGG
RFATSDLNDLYRRVINRNNRLRRLLELNAPDIIVRNEKRMLQESVDALLD
NGRRGRAIKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLK
LHQCGLPKKMALELFKPFVFAKLQRRGLATTIKAAKKLVEREEAEVWDIL
EEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFD
GDQMAVHVPLSLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYY
MSRALENKKGEGMVFANTSEVKRAYDNRVVELHAKVKVRITQVDVDRTSG
TSIVDTTVGRALLSEILPEGLPFQLANTEMTKKNISRLINSSYRLLGLKD
TVVFADKLMYTGYAYATRAGVSIGIDDMLIPDEKKGILTEAEAEVLEIQE
QYQSGLVTAGERYNKVVDIWSRTSERIAKAMMDTIGTEKVENAKGETIDQ
KSMNSLYIMADSGARGSQAQIRQLAGMRGLMARPDGSIIETPIKANFREG
LNVQEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEIDCGT
TEGLIMTPIVEGGDVVEPLKERVLGRVVAEDVVTRNTLLDEAWVAKLEDA
SVQSVKVRSTISCESSFGVCARCYGRDLARGHQVNIGEAVGVIAAQSIGE
PGTQLTDNITVKTTGSVKFNNLKAVSRSGELSVLDGHGRERERYKLPYGA
TITAAVKAGQSVANWDPGLPRVADLFEARKPKDPAILAERSGIISFGKDT
KGKQRLIIKDTDGSEHEELIPKYRQIIVFEGEHVTKGETVVDGEPSPQDI
LRLLGVEPLAAYLVKEIQDVYRLQGVKINDKHIEVITRQMLRKVEIVDQG
NSKFLNGEQVERQRVIEENARLVKRNELPAKYDPVLLGITKASLATESFI
SAASFQETTRVLTEAAVRGTRDNLRGLKENVIVGRLIPAGTGLAYHAGRR

3D structure

• PDB: 6j9e Structural basis for transcription antitermination at bacterial intrinsic terminator.
• Chain: D
• Resolution: 3.41 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	D	S210 E211 K332 K334 R352 A426 Y796 Q1327 E1328 R1331	S202 E203 K320 K322 R340 A414 Y779 Q1156 E1157 R1160
BS02	dna	D	Y46 R133 E1148 R1150	Y46 R133 E977 R979
BS03	rna	D	L252 L255 R425 D464	L244 L247 R413 D452
BS04	MG	D	D462 D464	D450 D452
BS05	ZN	D	C815 C897	C798 C870

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:6j9e, PDBe:6j9e, PDBj:6j9e
• PDBsum: 6j9e
• PubMed: 31296855
• UniProt: B2SQQ2|RPOC_XANOP DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)