Structure of PDB 8wut Chain A

Receptor sequence

>8wutA (length=1313) Species: 301447 (Streptococcus pyogenes serotype M1)

DKKYSIGLAIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGAL
LFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRL
EESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADL
RLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPI
NASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPN
FKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAIL
LSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIF
FDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRK
QRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYY
VGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKN
LPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDL
LFKTNRKVTVKQLKEDYFKKIETYHDLLKIIKDKDFLDNEENEDILEDIV
LTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGI
RDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSL
HEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMAREKNSR
ERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQEL
DINRLSDYDVDAIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKK
MKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQIT
KHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREI
NNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGKATAKYFFYSNIMNFFK
TEITIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQT
GGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKG
KSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYS
LFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDN
EQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPI
REQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSI
TGLYETRIDLSQL

3D structure

• PDB: 8wut Structural basis for pegRNA-guided reverse transcription by a prime editor.
• Chain: A
• Resolution: 3.0 Å

Enzymatic activity

• Enzyme Commision number: 3.1.-.-

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	A	L169 Y450 M495 T496 N497 K526 W659 M694 Q695 R778 R895 K902 K1107 E1108 S1109 K1151	L168 Y449 M494 T495 N496 K525 W639 M674 Q675 R750 R867 K874 K1055 E1056 S1057 K1099
BS02	dna	A	R1114 S1116 D1135 S1136 K1200 S1216 Q1221 A1320 R1333 R1335	R1062 S1064 D1083 S1084 K1148 S1164 Q1169 A1268 R1281 R1283
BS03	rna	A	K31 K33 L35 I43 K44 N46 E57 T58 A59 T62 R63 R66 R69 R70 R71 Y72 R74 R75 K76 N77 Y81 L101 S104 F105 H116 I122 H129 H160 K163 F164 R165 G166 Y325 H328 H329 K336 R340 F351 F352 Y359 I363 K401 Q402 R403 T404 F405 N407 R447 I448 Y450 L455 A456 R457 N459 S460 F462 R467 I473 K500 Y515 M694 H721 K742 R753 K929 M1089 P1090 Q1091 G1103 G1104 F1105 I1110 K1113 R1122 K1123 K1124 M1169 A1227 Q1272 H1349 Q1350 S1351 Y1356	K30 K32 L34 I42 K43 N45 E56 T57 A58 T61 R62 R65 R68 R69 R70 Y71 R73 R74 K75 N76 Y80 L100 S103 F104 H115 I121 H128 H159 K162 F163 R164 G165 Y324 H327 H328 K335 R339 F350 F351 Y358 I362 K400 Q401 R402 T403 F404 N406 R446 I447 Y449 L454 A455 R456 N458 S459 F461 R466 I472 K499 Y514 M674 H701 K722 R733 K901 M1037 P1038 Q1039 G1051 G1052 F1053 I1058 K1061 R1070 K1071 K1072 M1117 A1175 Q1220 H1297 Q1298 S1299 Y1304

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0004519 endonuclease activity
• GO:0004520 DNA endonuclease activity
• GO:0004527 exonuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0046872 metal ion binding

Biological Process

• GO:0043571 maintenance of CRISPR repeat elements
• GO:0051607 defense response to virus

External links

• PDB: RCSB:8wut, PDBe:8wut, PDBj:8wut
• PDBsum: 8wut
• PubMed: 38811740
• UniProt: Q99ZW2|CAS9_STRP1 CRISPR-associated endonuclease Cas9/Csn1 (Gene Name=cas9)