Structure of PDB 6wvj Chain D

Receptor sequence

>6wvjD (length=1176) Species: 1423 (Bacillus subtilis)

VNNFEYMNIGLASPDKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFG
PTKDWECHCGKYKRVRYKGVVCDRCGVEVTRAKVRRERMGHIELAAPVSH
IWYFKGIPSRMGLVLDMSPRALEEVIYFASYVVTDPANTPLEKKQLLSEK
EYRAYLDKYGNKFQASMGAEAIHKLLQDIDLVKEVDMLKEELKTSQGQRR
TRAIKRLEVLEAFRNSGNKPSWMILDVLPVIPPELRPMVQLDGGRFATSD
LNDLYRRVINRNNRLKRLLDLGAPSIIVQNEKRMLQEAVDALIDNGRRGR
PVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKMY
QCGLPKEMALELFKPFVMKELVEKGLAHNIKSAKRKIERVQPEVWDVLES
VIKEHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGD
QMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLT
LERAGAVGEGMVFKNTDEALLAYQNGYVHLHTRVAVAANSLKNVTFTEEQ
RSKLLITTVGKLVFNEILPESFPYMNEPTKSNIEEKTPDRFFLEKGADVK
AVIAQQPINAPFKKGILGKIIAEIFKRFHITETSKMLDRMKNLGFKYSTK
AGITVGVSDIVVLDDKQEILEEAQSKVDNVMKQFRRGLITEEERYERVIS
IWSAAKDVIQGKLMKSLDELNPIYMMSDSGARGNASNFTQLAGMRGLMAN
PAGRIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRR
LVDVAQDVIIRETDCGTDRGILAKPLKEGTETIERLEERLIGRFARKQVK
HPETGEVLVNENELIDEDKALEIVEAGIEEVWIRSAFTCNTPHGVCKRCY
GRNLATGSDVEVGEAVGIIAAQSIGEPGTQLTMRTGDDITQGLPRIQELF
EARNPKGQATITEIDGTVVEINEVRDKQQEIVVQGAVETRSYTAPYNSRL
KVAEGDKITRGQVLTEGSIDPKELLKVTDLTTVQEYLLHEVQKVYRMQGV
EIGDKHVEVMVRQMLRKVRVIDAGDTDVLPGTLLDIHQFTEANKKVLLEG
NRPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKGKRDELLG
LKENVIIGKLVPAGTGMMKYRKVKPV

3D structure

• PDB: 6wvj Molecular basis for RNA polymerase-dependent transcription complex recycling by the helicase-like motor protein HelD.
• Chain: D
• Resolution: 3.36 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	R328 R335 R341 T794 A795 Y799 Q1140	R325 R332 R338 T791 A792 Y796 Q1130
BS02	ZN	D	C60 C62 C75 C78	C57 C59 C72 C75
BS03	MG	D	D449 D451 D453	D446 D448 D450
BS04	ZN	D	C818 C892 C899 C902	C815 C889 C896 C899

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:0046677 response to antibiotic

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex

External links

• PDB: RCSB:6wvj, PDBe:6wvj, PDBj:6wvj
• PDBsum: 6wvj
• PubMed: 33339820
• UniProt: P37871|RPOC_BACSU DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)