Structure of PDB 5dqu Chain D

Receptor sequence

>5dquD (length=258) Species: 83333 (Escherichia coli K-12)

VSMIFLQYGQIDVIDGAFVLIDKTGIRTHIPVGSVACIMLEPGTRVSHAA
VRLAAQVGTLLVWVGEAGVRVYASGQPGGARSDKLLYQAKLALDEDLRLK
VVRKMFELRPAPARVEQLRGIEGSRVRATYALLAKQYGVTWNGRRYDPGD
TINQCISAATSCLYGVTEAAILAAGYAPAIGFVHTGKPLSFVYDIADIIK
FDTVVPKAFEIARRNPGEPDREVRLACRDIFRSSKTLAKLIPLIEDVLAA
GEIQPPAP

3D structure

• PDB: 5dqu Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems.
• Chain: D
• Resolution: 4.5 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	D	Y22 P56 E80 R84 Y86 S181 T184 S185 Y188 K211 Y217 D244 R248	Y8 P42 E66 R70 Y72 S157 T160 S161 Y164 K187 Y193 D220 R224
BS02	dna	D	Y22 D36 K37 R41 G57 R59	Y8 D22 K23 R27 G43 R45

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0004519 endonuclease activity
• GO:0004520 DNA endonuclease activity
• GO:0005515 protein binding
• GO:0008821 crossover junction DNA endonuclease activity
• GO:0017108 5'-flap endonuclease activity
• GO:0042802 identical protein binding
• GO:0042803 protein homodimerization activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006281 DNA repair
• GO:0006974 DNA damage response
• GO:0043571 maintenance of CRISPR repeat elements
• GO:0051607 defense response to virus
• GO:0099048 CRISPR-cas system

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5dqu, PDBe:5dqu, PDBj:5dqu
• PDBsum: 5dqu
• PubMed: 26478180
• UniProt: Q46896|CAS1_ECOLI CRISPR-associated endonuclease Cas1 (Gene Name=ygbT)