Structure of PDB 8qbk Chain U

Receptor sequence

>8qbkU (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: U
• 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	U	Y6 F10 R13 N14	Y4 F8 R11 N12
BS02	dna	U	E35 R38 L39 F46 R47 Y51 Q67 P68 K73 F96 I102 A129 N130 K131 F133 G134 S138 R143 S147 T150 K151 K156 K176 R180 G183 Y184 R188 Y195 D197 D198 K211 F215 I219 T244 H280 G283 W284 F287	E33 R36 L37 F44 R45 Y49 Q65 P66 K71 F94 I100 A127 N128 K129 F131 G132 S136 R141 S145 T148 K149 K154 K174 R178 G181 Y182 R186 Y193 D195 D196 K209 F213 I217 T242 H278 G281 W282 F285
BS03	rna	U	K56 R63 I65 K73 R81 F96 E97 H99 Q100 Q161 G162 A163 P164 P167 M206 K231 C233 I234 S235 G236 P237 R238 S239 Q240 V247 S249 R257 E258 K261 R264 G283 S286 S290 R298	K54 R61 I63 K71 R79 F94 E95 H97 Q98 Q159 G160 A161 P162 P165 M204 K229 C231 I232 S233 G234 P235 R236 S237 Q238 V245 S247 R255 E256 K259 R262 G281 S284 S288 R296
BS04	rna	U	S218 P221	S216 P219

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)