Structure of PDB 5d08 Chain B

Receptor sequence

>5d08B (length=375) Species: 224308 (Bacillus subtilis subsp. subtilis str. 168)

NVYQLKEELIEYAKSIGVDKIGFTTADTFDSLKDRLILQESLGYLSGFEE
PDIEKRVTPKLLLPKAKSIVAIALAYPSRMKDAPRSTRTERRGIFCRASW
GKDYHDVLREKLDLLEDFLKSKHEDIRTKSMVDTGELSDRAVAERAGIGF
SAKNCMITTPEYGSYVYLAEMITNIPFEPDVPIEDMCGSCTKCLDACPTG
ALVNPGQLNAQRCISFLTQTKGFLPDEFRTKIGNRLYGCDTCQTVCPLNK
GKDFHLHPEMEPDPEIAKPLLKPLLAISNREFKEKFGHVSGSWRGKKPIQ
RNAILALAHFKDASALPELTELMHKDPRPVIRGTAAWAIGKIGDPAYAEE
LEKALEKEKDEEAKLEIEKGIELLK

3D structure

• PDB: 5d08 Molecular basis of cobalamin-dependent RNA modification.
• Chain: B
• Resolution: 1.747 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	K153 N154 C187 C190 C193 C246 P247 L248
BS02	SF4	B	C198 P199 L203 C214 I215 C240 C243	C197 P198 L202 C213 I214 C239 C242
BS03	B12	B	R36 F49 E50 R57 C97 D134 S139 D140 R141 A142 S152 M157 I158 V167 L169 L209 S216 F217 G239 C240	R35 F48 E49 R56 C96 D133 S138 D139 R140 A141 S151 M156 I157 V166 L168 L208 S215 F216 G238 C239

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:5d08, PDBe:5d08, PDBj:5d08
• PDBsum: 5d08
• PubMed: 27638883
• UniProt: P97030|QUEG_BACSU Epoxyqueuosine reductase (Gene Name=queG)