Structure of PDB 6k0g Chain A

Receptor sequence

>6k0gA (length=335) Species: 565042 (Bifidobacterium longum subsp. longum JCM 1217)

TTVLVTGGAGFIATHTDIELLNKGYDVISVDNYGNSSPVALERVEQITGK
PVKRYDGDVRDEALMERVFAENNIDWVIHFAGLKAVGESVAKPIEYYDNN
LYSTLVLLKVMKKHNVKKIIFSSSATVYGTPKELPITEETPTGGTTNPYG
TSKLFQEQILRDVHVADPSWTIVLLRYFNPVGAHESGLLGEDPKGIPANL
TPYVAKVAVGELKEVQVYGDDYDTPDGTGVRDYIHVVDLAKGHVAVIDHI
DKEGVFVYNLGTGHGYSVLEVIKAYEKAAGHPIPYAIKPRRPGDIAACYA
DASKAEKELGWKAELTIDDMAASSLNWQTKNPNGF

3D structure

• PDB: 6k0g Structural basis for broad substrate specificity of UDP-glucose 4-epimerase in the human milk oligosaccharide catabolic pathway of Bifidobacterium longum.
• Chain: A
• Resolution: 1.8 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): S125 A126 T127 Y150 K154
• Catalytic site (residue number reindexed from 1): S124 A125 T126 Y149 K153
• Enzyme Commision number: 5.1.3.2: UDP-glucose 4-epimerase.

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	UDP	A	N180 A199 N200 L201 Q217 V218 Y219 R232 Y234 V269 R292 D295	N179 A198 N199 L200 Q216 V217 Y218 R231 Y233 V268 R291 D294
BS02	NAD	A	G8 G11 F12 I13 D32 N33 N36 S37 D59 V60 F81 A82 G83 K85 N100 S123 S124 Y150 K154 Y178 P181	G7 G10 F11 I12 D31 N32 N35 S36 D58 V59 F80 A81 G82 K84 N99 S122 S123 Y149 K153 Y177 P180
BS03	MG	A	E67 H115	E66 H114

Gene Ontology

Molecular Function

• GO:0003978 UDP-glucose 4-epimerase activity
• GO:0016853 isomerase activity

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0006012 galactose metabolic process
• GO:0033499 galactose catabolic process via UDP-galactose

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:6k0g, PDBe:6k0g, PDBj:6k0g
• PDBsum: 6k0g
• PubMed: 31366978
• UniProt: E8MF10|GALE_BIFL2 UDP-glucose 4-epimerase (Gene Name=lnpD)