Structure of PDB 6gtf Chain A

Receptor sequence

>6gtfA (length=1280) Species: 401614 (Francisella tularensis subsp. novicida U112)

IYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDDEKRAKDYKKAKQ
IIDKYHQFFIEEILSSVCISEDLLQNYSDVYFKLKKSDDDNLQKDFKSAK
DTIKKQISEYIKDSEKFKNLFNQNLIDAKKGQESDLILWLKQSKDNGIEL
FKANSDITDIDEALEIIKSFKGWTTYFKGFHENRKNVYSSNDIPTSIIYR
IVDDNLPKFLENKAKYESLKDKAPEAINYEQIKKDLAEELTFDIDYKTSE
VNQRVFSLDEVFEIANFNNYLNQSGITKFNTIIGGKFVNGENTKRKGINE
YINLYSQQINDKTLKKYKMSVLFKQILSDTESKKLEDDSDVVTTMQSFYE
QIAAFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSLTDLSQQVF
DDYSVIGTAVLEYITQQIAPKNLDNPSKKEQELIAKKTEKAKYLSLETIK
LALEEFNKHRDIDKQCRFEEILANFAAIPMIFDEIAQNKDNLAQISIKYQ
NQGKKDLLQASAEDDVKAIKDLLDQTNNLLHKLKIFHISQSEDKANILDK
DEHFYLVFEECYFELANIVPLYNKIRNYITQKPYSDEKFKLNFENSTLAN
GWDKNKEPDNTAILFIKDDKYYLGVMNKKNNKIFDDKAIKENKGEGYKKI
VYKLLPGANKMLPKVFFSAKSIKFYNPSEDILRIRNHSTHTKNGSPQKGY
EKFEFNIEDCRKFIDFYKQSISKHPEWKDFGFRFSDTQRYNSIDEFYREV
ENQGYKLTFENISESYIDSVVNQGKLYLFQIYNKDFSAYSKGRPNLHTLY
WKALFDERNLQDVVYKLNGEAELFYRKQSIPKKITHPAKEAIANKNKDNP
KKESVFEYDLIKDKRFTEDKFFFHCPITINFKSSGANKFNDEINLLLKEK
ANDVHILSIDRGERHLAYYTLVDGKGNIIKQDTFNIIGNDRMKTNYHDKL
AAIEKDRDSARKDWKKINNIKEMKEGYLSQVVHEIAKLVIEYNAIVVFQD
LNVYQKLEKMLIEKLNYLVFKDNEFDKTGGVLRAYQLTAPFETFKKMGKQ
TGIIYYVPAGFTSKICPVTGFVNQLYPKYESVSKSQEFFSKFDKICYNLD
KGYFEFSFDYKNFGDKAAKGKWTIASFGSRLINFRNSDKNHNWDTREVYP
TKELEKLLKDYSIEYGHGECIKAAICGESDKKFFAKLTSVLNTILQMRNS
KTGTELDYLISPVADVNGNFFDSRQAPKNMPQDADANGAYHIGLKGLMLL
GRIKNNQEGKKLNLVIKNEEYFEFVQNRNN

3D structure

• PDB: 6gtf Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity.
• Chain: A
• Resolution: 3.63 Å

Enzymatic activity

• Enzyme Commision number: 3.1.21.1: deoxyribonuclease I.
  4.6.1.22: Bacillus subtilis ribonuclease.

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	S14 K15 T16 R18 E20 K51 N185 R186 R202 F325 K326 K589 Y591 K595 N790 K791 Y796 S797 K798 R800 N802 L803 H804 R833 H843 I849 N853 F863 Y865 L867 I868 K869 K871 R872 F873 F879 H881 R948 M949 T951 Y953 K956 M980 G983 S986 H990 K1034 K1041	S12 K13 T14 R16 E18 K49 N183 R184 R200 F323 K324 K582 Y584 K588 N783 K784 Y789 S790 K791 R793 N795 L796 H797 R826 H836 I842 N846 F856 Y858 L860 I861 K862 K864 R865 F866 F872 H874 R941 M942 T944 Y946 K949 M973 G976 S979 H983 K1014 K1021
BS02	dna	A	N185 G608 D610 N612 K613 L661 P663 M668 K671 V672 S675 A676 K677 W734 K823 N825 E827 T1063 F1064 K1065 K1066	N183 G601 D603 N605 K606 L654 P656 M661 K664 V665 S668 A669 K670 W727 K816 N818 E820 T1043 F1044 K1045 K1046
BS03	dna	A	N124 Q125 G174 N666 K667 P670 K671 T698 K699 G701 I750 D751	N122 Q123 G172 N659 K660 P663 K664 T691 K692 G694 I743 D744

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0004519 endonuclease activity
• GO:0004530 deoxyribonuclease I activity
• GO:0016829 lyase activity

Biological Process

• GO:0006259 DNA metabolic process
• GO:0051607 defense response to virus

External links

• PDB: RCSB:6gtf, PDBe:6gtf, PDBj:6gtf
• PDBsum: 6gtf
• PubMed: 30503205
• UniProt: A0Q7Q2|CS12A_FRATN CRISPR-associated endonuclease Cas12a (Gene Name=cas12a)