Structure of PDB 8hyj Chain A

Receptor sequence

>8hyjA (length=1141) Species: 3702 (Arabidopsis thaliana)

GITFALASHHEICIQSISESAINHPSQLTNAFLGLPLEFGKCESCGATEP
DKCEGHFGYIQLPVPIYHPAHVNELKQMLSLLCLKCLKIKEASQISIKDR
ASDGASYLELKLPSRSRLQPGCWNFLERYGYRYGSDYTRPLLAREVKEIL
RRIPEESRKKLTAKGHIPQEGYILEYLPVPPNCLSPSRIELKDVLKKVIA
IKSSRSGETNFESHKAEASEMFRVVDTYLKGSGFSSRSVITGDAYRHVNE
VGIPIEIAQRITFEERVSVHNRGYLQKLVDDKLCLSYTQGSTTYSLRDGS
KGHTELKPGQVVHRRVMDGDVVFINRPPTTHKHSLQALRVYVHEDNTVKI
NPLMCSPLSADFDGDCVHLFYPQSLSAKAEVMELFSVEKQLLSSHTGQLI
LQMGSDSLLSLRVMLERVFLDKATAQQLAMYGSLSLPPPALRKSSKSGPA
WTVFQILQLAFPERLSCKGDRFLVDGSDLLKFDFGVDAMGSIINEIVTSI
FLEKGPKETLGFFDSLQPLLMESLFAEGFSLSLEDLSMSRADMDVIHNLI
IREISPMVSRLRLSYRDELQLENSIHKVKEVAANFMLKSYSIRNLIDIKS
NSAITKLVQQTGFLGLQLSDKKKFYTKTLVEDMAIFCKRKYGRISSSGDF
GIVKGCFFHGLDPYEEMAHSIAAREVIVRSSRGLAEPGTLFKNLMAVLRD
IVITNDGTVRNTCSNSVIQFKYGVDSERGHQGLFEAGEPVGVLAATAMSN
PAYKAVLDSSPNSNSSWELMKEVLLCKVNFQNTTNDRRVILYLNECHCGK
RFCQENAACTVRNKLNKVSLKDTAVEFLVEYRKQGIDSCLHGHIHLNKTL
LQDWNISMQDIHQKCEDVINSLGQKKKKKATDDFKRTSLSVSECCSFRDP
CGSKGSDMPCLTFSYNATDPDLERTLDVLCNTVYPVLLEIVIKGDSRICS
ANIIWNSSDMTTWIRNRHASRRGEWVLDVTVEKSAVKQSGDAWRVVIDSC
LSVLHLIDTKRSIPYSVKQVQELLGLSCAFEQAVQRLSASVRMVSKGVLK
EHIILLANNMTCSGTMLGFNSGGYKALTRSLNIKAPFTEATLIAPRKCFE
KAAEKCHTDSLSTVVGSCSWGKRVDVGTGSQFELLWNQKET

3D structure

• PDB: 8hyj A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex.
• Chain: A
• Resolution: 4.3 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	A	D451 D453	D363 D365
BS02	dna	A	R325 L772 A773 K780	R237 L684 A685 K692
BS03	MG	A	D451 D453	D363 D365

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0005515 protein 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:0030422 siRNA processing
• GO:0035194 regulatory ncRNA-mediated post-transcriptional gene silencing
• GO:0050832 defense response to fungus

Cellular Component

• GO:0000418 RNA polymerase IV complex
• GO:0000419 RNA polymerase V complex
• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005634 nucleus
• GO:0005730 nucleolus
• GO:0016604 nuclear body
• GO:0030880 RNA polymerase complex

External links

• PDB: RCSB:8hyj, PDBe:8hyj, PDBj:8hyj
• PDBsum: 8hyj
• PubMed: 37253723
• UniProt: Q5D869|NRPE1_ARATH DNA-directed RNA polymerase V subunit 1 (Gene Name=NRPE1)