Structure of PDB 6wvk Chain D

Receptor sequence

>6wvkD (length=1184) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

VNNFEYMNIGLASPDKIRSWSFGEVKKPETINYRTLKPEKDGLFCERIFG
PTKDWECHCGKYKRVRYKGVVCDRCGVEVTRAKVRRERMGHIELAAPVSH
IWYFKGIPSRMGLVLDMSPRALEEVIYFASYVVTDPANTPLEKKQLLSEK
EYRAYLDKYGNKFQASMGAEAIHKLLQDIDLVKEVDMLKEELKTSQGQRR
TRAIKRLEVLEAFRNSGNKPSWMILDVLPVIPPELRPMVQLDGGRFATSD
LNDLYRRVINRNNRLKRLLDLGAPSIIVQNEKRMLQEAVDALIDNGRRGR
PVTGPGNRPLKSLSHMLKGKQGRFRQNLLGKRVDYSGRSVIVVGPHLKMY
QCGLPKEMALELFKPFVMKELVEKGLAHNIKSAKRKIERVQPEVWDVLES
VIKEHPVLLNRAPTLHRLGIQAFEPTLVEGRAIRLHPLVCTAYNADFDGD
QMAVHVPLSAEAQAEARILMLAAQNILNPKDGKPVVTPSQDMVLGNYYLT
LERAGAVGEGMVFKNTDEALLAYQNGYVHLHTRVAVAANSLKNVTFTEEQ
RSKLLITTVGKLVFNEILPESFPYMNEPTKSNIEEKTPDRFFLEKGADVK
AVIAQQPINAPFKKGILGKIIAEIFKRFHITETSKMLDRMKNLGFKYSTK
AGITVGVSDIVVLDDKQEILEEAQSKVDNVMKQFRRGLITEEERYERVIS
IWSAAKDVIQGKLMKSLDELNPIYMMSDSGARGNASNFTQLAGMRGLMAN
PAGRIIELPIKSSFREGLTVLEYFISTHGARKGLADTALKTADSGYLTRR
LVDVAQDVIIRETDCGTDRGILAKPLKEGTETIERLEERLIGRFARKQVK
HPETGEVLVNENELIDEDKALEIVEAGIEEVWIRSAFTCNTPHGVCKRCY
GRNLATGSDVEVGEAVGIIAAQSIGEPGTQLTMRTFHTGGVAGDDITQGL
PRIQELFEARNPKGQATITEIDGTVVEINEVRDKQQEIVVQGAVETRSYT
APYNSRLKVAEGDKITRGQVLTEGSIDPKELLKVTDLTTVQEYLLHEVQK
VYRMQGVEIGDKHVEVMVRQMLRKVRVIDAGDTDVLPGTLLDIHQFTEAN
KKVLLEGNRPATGRPVLLGITKASLETDSFLSAASFQETTRVLTDAAIKG
KRDELLGLKENVIIGKLVPAGTGMMKYRKVKPVS

3D structure

• PDB: 6wvk 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	ZN	D	C60 C62 C75 C78	C57 C59 C72 C75
BS02	MG	D	D449 D451 D453	D446 D448 D450
BS03	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:6wvk, PDBe:6wvk, PDBj:6wvk
• PDBsum: 6wvk
• PubMed: 33339820
• UniProt: P37871|RPOC_BACSU DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)