Structure of PDB 5th5 Chain D

Receptor sequence

>5th5D (length=241) Species: 1423 (Bacillus subtilis)

KGIPVLEIFGPTIQGEGMVIGQKTMFVRTAGCDYSCSWCDSAFTWDGSAK
KDIRWMTAEEIFAELKDIGGDAFSHVTISGGNPALLKQLDAFIELLKENN
IRAALETQGTVYQDWFTLIDDLTISPKPPSSKMVTNFQKLDHILTSLQEN
DRQHAVSLKVVIFNDEDLEFAKTVHKRYPGIPFYLQVGNDDVHTTDDQSL
IAHLLGKYEALVDKVAVDAELNLVRVLPQLHTLLWGNKRGV

3D structure

• PDB: 5th5 7-Carboxy-7-deazaguanine Synthase: A Radical S-Adenosyl-l-methionine Enzyme with Polar Tendencies.
• Chain: D
• Resolution: 2.407 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): F28 C34 C41 D42 S43 E108
• Catalytic site (residue number reindexed from 1): F26 C32 C39 D40 S41 E106
• Enzyme Commision number: 4.3.99.3: 7-carboxy-7-deazaguanine synthase.

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	SF4	D	C34 Y36 C38 C41 W47 G83 Q110 K129	C32 Y34 C36 C39 W45 G81 Q108 K127
BS02	7C5	D	I15 Q16 E18 F28 R30 W40 D42 S127 K161 V163 Q188 N191 Q231 H233 V243	I13 Q14 E16 F26 R28 W38 D40 S125 K159 V161 Q186 N189 Q229 H231 V241
BS03	MET	D	G82 G83 E108 T109 Q110 K129	G80 G81 E106 T107 Q108 K127

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0016829 lyase activity
• GO:0016840 carbon-nitrogen lyase activity
• GO:0042803 protein homodimerization activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:1904047 S-adenosyl-L-methionine binding

Biological Process

• GO:0008616 queuosine biosynthetic process

External links

• PDB: RCSB:5th5, PDBe:5th5, PDBj:5th5
• PDBsum: 5th5
• PubMed: 28045519
• UniProt: O31677|QUEE_BACSU 7-carboxy-7-deazaguanine synthase (Gene Name=queE)