Structure of PDB 6gtd Chain A

Receptor sequence

>6gtdA (length=1269) Species: 401614 (Francisella tularensis subsp. novicida U112)

MSIYQEFVNKYSLSKTLRFELIPQGKTLENIKARGLILDDEKRAKDYKKA
KQIIDKYHQFFIEEILSSVCISEDLLQNYSDVYFKLKKSDDDNLQKDFKS
AKDTIKKQISEYIKDSEKFKNLFNQNLIDAKKGQESDLILWLKQSKDNGI
ELFKANSDITDIDEALEIIKSFKGWTTYFKGFHENRKNVYSSNDIPTSII
YRIVDDNLPKFLENKAKYESLKDKAPEAINYEQIKKDLAEELTFDIDYKT
SEVNQRVFSLDEVFEIANFNNYLNQSGITKFNTIIGGKFVNGENTKRKGI
NEYINLYSQQINDKTLKKYKMSVLFKQILSDTDKLEDDSDVVTTMQSFYE
QIAAFKTVEEKSIKETLSLLFDDLKAQKLDLSKIYFKNDKSLTDLSQQVF
DDYSVIGTAVLEYITQQIAPKNQELIAKKTEKAKYLSLETIKLALEEFNK
HRDIDKQCRFEEILANFAAIPMIFDEIAQNKDNLAQISIKYQNQGKKDLL
QASAEDDVKAIKDLLDQTNNLLHKLKIFHISQSEDKANILDKDEHFYLVF
EECYFELANIVPLYNKIRNYITQKPYSDEKFKLNFENSTLANGWDKNKEP
DNTAILFIKDDKYYLGVMNKKNNKIFDDKAIKENKGEGYKKIVYKLLPGA
NKMLPKVFFSAKSIKFYNPSEDILRIRNHSTHTKNGSPQKGYEKFEFNIE
DCRKFIDFYKQSISKHPEWKDFGFRFSDTQRYNSIDEFYREVENQGYKLT
FENISESYIDSVVNQGKLYLFQIYNKDFSAYSKGRPNLHTLYWKALFDER
NLQDVVYKLNGEAELFYRKQSIPKKITHPAKEAIANKNKDNPKKESVFEY
DLIKDKRFTEDKFFFHCPITINFKSSGANKFNDEINLLLKEKANDVHILS
IDRGERHLAYYTLVDGKGNIIKQDTFNIIGNDRMKTNYHDKLAAIEKDRD
SARKDWKKINNIKEMKEGYLSQVVHEIAKLVIEYNAIVVFQDLNKQVYQK
LEKMLIEKLNYLVFKDNEFDKTGGVLRAYQLTAPFETFKKMGKQTGIIYY
VPAGFTSKICPVTGFVNQLYPKYESVSKSQEFFSKFDKICYNLDKGYFEF
SFDYKNFGDKAAKGKWTIASFGSRLINFRNSNWDTREVYPTKELEKLLKD
YSIEYGHGECIKAAICGESDKKFFAKLTSVLNTILQMRNSKTGTELDYLI
SPVADVNGNFFDSRQAPKNMPQDADANGAYHIGLKGLMLLGRIKNNQEGK
KLNLVIKNEEYFEFVQNRN

3D structure

• PDB: 6gtd Conformational Activation Promotes CRISPR-Cas12a Catalysis and Resetting of the Endonuclease Activity.
• Chain: A
• Resolution: 4.24 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 P577 S797 K798 G799 R800 L803 H804 H843 I849 A850 K852 N853 V862 F863 Y865 L867 I868 K869 D870 K871 R872 R948 S986 Q987	S14 K15 T16 P562 S782 K783 G784 R785 L788 H789 H828 I834 A835 K837 N838 V847 F848 Y850 L852 I853 K854 D855 K856 R857 R933 S971 Q972
BS02	dna	A	N185 Y579 N580 L661 V672 S675 A676 G826 T1063 F1064 K1065	N185 Y564 N565 L646 V657 S660 A661 G811 T1037 F1038 K1039
BS03	dna	A	Q125 N666 K667 K699 N700 I750 N894 K895 K1280	Q125 N651 K652 K684 N685 I735 N879 K880 K1250

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