Structure of PDB 6j9f Chain D

Receptor sequence

>6j9fD (length=1215) Species: 360094 (Xanthomonas oryzae pv. oryzae PXO99A)

MKDLLNLFNQQRQTLDFDAIKIALASPDLIRSWSYGEVKKPETINYRTFK
PERDGLFCAAIFGPIKDYECLCGKYKRMKHRGVVCEKCGTEVTLAKVRRE
RMGHIDLASPVAHIWFLKSLPSRIGLMLDMTLRDIERVLYFEAYVVTRRQ
LLTEEQYLTARQEYNDDFDAAMGAEAVYELLRTIDLQSEMTRLREEIAST
GSETKLKRLTKRIKLIEAFLESGNRPEWMVMTVLPVLPPDLRPLVPLDGG
RFATSDLNDLYRRVINRNNRLRRLLELNAPDIIVRNEKRMLQESVDALLD
NGRRGRAIKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLK
LHQCGLPKKMALELFKPFVFAKLQRRGLATTIKAAKKLVEREEAEVWDIL
EEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCTAFNADFD
GDQMAVHVPLSLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYY
MSRALENKKGEGMVFANTSEVKRAYDNRVVELHAKVKVRITQVDVDKRTS
GTSIVDTTVGRALLSEILPEGLPFQLANTEMTKKNISRLINSSYRLLGLK
DTVVFADKLMYTGYAYATRAGVSIGIDDMLIPDEKKGILTEAEAEVLEIQ
EQYQSGLVTAGERYNKVVDIWSRTSERIAKAMMDTIGTEKVENAKGETID
QKSMNSLYIMADSGARGSQAQIRQLAGMRGLMARPDGSIIETPIKANFRE
GLNVQEYFNSTHGARKGLADTALKTANSGYLTRRLVDVAQDVVITEIDCG
TTEGLIMTPIVEGGDVVEPLKERVLGRVVAEDVVTRNTLLDEAWVAKLED
ASVQSVKVRSTISCESSFGVCARCYGRDLARGHQVNIGEAVGVIAAQSIG
EPGTQLTDNITVKTTGSVKFNNLKSVAHASGSLVAVSRSGELSVLDGHGR
ERERYKLPYGATITAKDGDAVKAGQSVANWDPGLPRVADLFEARKPKDPA
ILAERSGIISFGKDTKGKQRLIIKDTDGSEHEELIPKYRQIIVFEGEHVT
KGETVVDGEPSPQDILRLLGVEPLAAYLVKEIQDVYRLQGVKINDKHIEV
ITRQMLRKVEIVDQGNSKFLNGEQVERQRVIEENARLVKRNELPAKYDPV
LLGITKASLATESFISAASFQETTRVLTEAAVRGTRDNLRGLKENVIVGR
LIPAGTGLAYHAGRR

3D structure

• PDB: 6j9f Structural basis for transcription antitermination at bacterial intrinsic terminator.
• Chain: D
• Resolution: 3.95 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	Y46 F260 T262 K332 K334 R339 T791 Y796	Y46 F252 T254 K320 K322 R327 T775 Y780
BS02	dna	D	Y46 R1150	Y46 R994
BS03	rna	D	V253 L255 A261 R322 R425 D464	V245 L247 A253 R310 R413 D452
BS04	MG	D	D460 D462 D464	D448 D450 D452
BS05	ZN	D	C85 C88	C85 C88
BS06	ZN	D	C815 C890 C900	C799 C864 C874

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:6j9f, PDBe:6j9f, PDBj:6j9f
• PDBsum: 6j9f
• PubMed: 31296855
• UniProt: B2SQQ2|RPOC_XANOP DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)