Structure of PDB 1ker Chain A

Receptor sequence

>1kerA (length=346) Species: 1307 (Streptococcus suis)

QFKNIIVTGGAGFIGSNFVHYVYNNHPDVHVTVLDKLTYAGNKANLEAIL
GDRVELVVGDIADAELVDKLAAKADAIVHYAAESHNDNSLNDPSPFIHTN
FIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAE
TNYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFI
PRQITNILAGIKPKLYGEGKNVRDWIHTNDHSTGVWAILTKGRMGETYLI
GADGEKNNKEVLELILEKMGQPKDAYDHVTDRAGHDLRYAIDASKLRDEL
GWTPQFTDFSEGLEETIQWYTDNQDWWKAEKEAVEANYAKTQEVIK

3D structure

• PDB: 1ker Toward a structural understanding of the dehydratase mechanism.
• Chain: A
• Resolution: 2.2 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): T125 D126 E127 Y161 K165
• Catalytic site (residue number reindexed from 1): T123 D124 E125 Y159 K163
• Enzyme Commision number: 4.2.1.46: dTDP-glucose 4,6-dehydratase.

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	DAU	A	S86 N88 T125 D126 E127 Y161 N190 K200 F201 R204 Q205 K216 L217 Y218 R225 N260 R284 H287	S84 N86 T123 D124 E125 Y159 N188 K198 F199 R202 Q203 K214 L215 Y216 R223 N258 R282 H285
BS02	NAD	A	G14 F15 I16 D37 K38 L39 T40 A42 G43 D62 I63 Y82 A83 A84 S86 T101 V123 S124 T125 Y161 K165 C188 N191	G12 F13 I14 D35 K36 L37 T38 A40 G41 D60 I61 Y80 A81 A82 S84 T99 V121 S122 T123 Y159 K163 C186 N189

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0008460 dTDP-glucose 4,6-dehydratase activity
• GO:0016829 lyase activity

Biological Process

• GO:0009225 nucleotide-sugar metabolic process

External links

• PDB: RCSB:1ker, PDBe:1ker, PDBj:1ker
• PDBsum: 1ker
• PubMed: 11796113
• UniProt: Q8GIP9