Structure of PDB 5d0b Chain B

Receptor sequence

>5d0bB (length=375) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

NVYQLKEELIEYAKSIGVDKIGFTTADTFDSLKDRLILQESLGYLSGFEE
PDIEKRVTPKLLLPKAKSIVAIALAYPSRMKDAPRSTRTERRGIFCRASW
GKDYHDVLREKLDLLEDFLKSKHDIRTKSMVDTGELSDRAVAERAGIGFS
AKNCMITTPEYGSYVYLAEMITNIPFEPDVPIEDMCGSCTKCLDACPTGA
LVNPGQLNAQRCISFLTQTKGFLPDEFRTKIGNRLYGCDTCQTVCPLNKG
KDFHLHPEMEPDPEIAKPLLKPLLAISNREFKEKFGHVSGSWRGKKPIQR
NAILALAHFKDASALPELTELMHKDPRPVIRGTAAWAIGKIGDPAYAEEL
EKALEKEKDEEAKLEIEKGIELLKA

3D structure

• PDB: 5d0b Molecular basis of cobalamin-dependent RNA modification.
• Chain: B
• Resolution: 2.645 Å

Enzymatic activity

• Enzyme Commision number: 1.17.99.6: epoxyqueuosine reductase.

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	B	K154 N155 C188 C191 C194 C247 P248 L249	K152 N153 C186 C189 C192 C245 P246 L247
BS02	SF4	B	C198 P199 C214 I215 C240 C243	C196 P197 C212 I213 C238 C241
BS03	B12	B	R36 F49 E50 R57 C97 Y105 D134 S139 D140 R141 A142 S152 M157 I158 V167 L169 G207 L209 S216 G239 C240	R35 F48 E49 R56 C96 Y104 D132 S137 D138 R139 A140 S150 M155 I156 V165 L167 G205 L207 S214 G237 C238

Gene Ontology

Molecular Function

• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0052693 epoxyqueuosine reductase activity

Biological Process

• GO:0006400 tRNA modification
• GO:0008033 tRNA processing
• GO:0008616 queuosine biosynthetic process

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:5d0b, PDBe:5d0b, PDBj:5d0b
• PDBsum: 5d0b
• PubMed: 27638883
• UniProt: P97030|QUEG_BACSU Epoxyqueuosine reductase (Gene Name=queG)