Structure of PDB 8exa Chain A

Receptor sequence

>8exaA (length=341) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

IRNKAFVVRLYPNAAQTELINRTLGSARFVYNHFLARRIAAYKESGKGLT
YGQTSSELTLLKQAEETSWLSEVDKFALQNSLKNLETAYKNFFRTVKQSG
KKVGFPRFRKKRTGESYRTQFTNNNIQIGEGRLKLPKLGWVKTKGQQDIQ
GKILNVTVRRIHEGHYEASVLCEVEIPYLPAAPKFAAGVDVGIKDFAIVT
DGVRFKHEQNPKYYRSTLKRLRKAQQTLSRRKKGSARYGKAKTKLARIHK
RIVNKRQDFLHKLTTSLVREYEIIGTEHLKPDNMRKNRRLALSISDAGWG
EFIRQLEYKAAWYGRLVSKVSPDRDENAALNIRREALVAAG

3D structure

• PDB: 8exa TnpB structure reveals minimal functional core of Cas12 nuclease family.
• Chain: A
• Resolution: 3.14 Å

Enzymatic activity

• Enzyme Commision number: 3.1.21.-

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	K5 A6 Y12 N85 G105 P107 R108 R110 S117 G146 Q148 T158 R160 S170 Y215 R223 Q226 Q227 S230 R231 R232 K233 S236 A237 R238 K241 R252 K256 D259 K263 T266 R270 D283 R286 R289 A292 L293 Y309 K310 W313	K4 A5 Y11 N84 G104 P106 R107 R109 S116 G145 Q147 T157 R159 S169 Y214 R222 Q225 Q226 S229 R230 R231 K232 S235 A236 R237 K240 R251 K255 D258 K262 T265 R269 D282 R285 R288 A291 L292 Y308 K309 W312
BS02	dna	A	Y43 K48 T60 K63 K76 F77 Q80 F94 F106 K135 P137 K138	Y42 K47 T59 K62 K75 F76 Q79 F93 F105 K134 P136 K137
BS03	dna	A	T114 Q121 T123 N156 L172 K234 K243 H250 V254 P282 R286 G299 W300 G301 E302	T113 Q120 T122 N155 L171 K233 K242 H249 V253 P281 R285 G298 W299 G300 E301

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0004519 endonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006310 DNA recombination
• GO:0032196 transposition

External links

• PDB: RCSB:8exa, PDBe:8exa, PDBj:8exa
• PDBsum: 8exa
• PubMed: 37020015
• UniProt: Q7DF80|DRA2B_DEIRA RNA-guided DNA endonuclease TnpB (Gene Name=tnpB)