Structure of PDB 8qbk Chain K

Receptor sequence

>8qbkK (length=309) Species: 469008 (Escherichia coli BL21(DE3))

SAEYLNTFRLRNLGLPVMNNLHDMSKATRISVETLRLLIYTADFRYRIYT
VEKKGPEKRMRTIYQPSRELKALQGWVLRNILDKLSSSPFSIGFEKHQSI
LNNATPHIGANFILNIDLEDFFPSLTANKVFGVFHSLGYNRLISSVLTKI
CCYKNLLPQGAPSSPKLANLICSKLDYRIQGYAGSRGLIYTRYADDLTLS
AQSMKKVVKARDFLFSIIPSEGLVINSKKTCISGPRSQRKVTGLVISQEK
VGIGREKYKEIRAKIHHIFCGKSSEIEHVRGWLSFILSVDSKSHRRLITY
ISKLEKKYG

3D structure

• PDB: 8qbk Retron-Eco1 assembles NAD + -hydrolyzing filaments that provide immunity against bacteriophages.
• Chain: K
• Resolution: 2.99 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.49: RNA-directed DNA 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	K	E35 R38 L39 Y42 T43 F46 R49 Y51 Q67 P68 R70 I102 A129 K131 F133 S138 R143 S147 T150 K151 K176 R180 G183 Y184 R188 Y195 D197 D198 K211 F215 I219 T244 G283 W284 F287	E33 R36 L37 Y40 T41 F44 R47 Y49 Q65 P66 R68 I100 A127 K129 F131 S136 R141 S145 T148 K149 K174 R178 G181 Y182 R186 Y193 D195 D196 K209 F213 I217 T242 G281 W282 F285
BS02	rna	K	K56 R63 I65 K73 R81 F96 E97 H99 Q100 A163 P164 P167 K230 C233 P237 R238 S239 Q240 S249 K252 R257 K261 R264 A265 G283 S286 S290 R298	K54 R61 I63 K71 R79 F94 E95 H97 Q98 A161 P162 P165 K228 C231 P235 R236 S237 Q238 S247 K250 R255 K259 R262 A263 G281 S284 S288 R296
BS03	rna	K	S218 P221	S216 P219
BS04	dna	K	Y6 L7 F10 R13 N14	Y4 L5 F8 R11 N12

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0003964 RNA-directed DNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006974 DNA damage response
• GO:0051607 defense response to virus

External links

• PDB: RCSB:8qbk, PDBe:8qbk, PDBj:8qbk
• PDBsum: 8qbk
• PubMed: 38788717
• UniProt: P23070|RT86_ECOLX Retron Ec86 reverse transcriptase (Gene Name=ret)