Structure of PDB 4ptn Chain D

Receptor sequence

>4ptnD (length=298) Species: 83333 (Escherichia coli K-12)

ALFTGIIPPVSTIFTADGQLDKPGTAALIDDLIKAGVDGLFFLGSGGEFS
QLGAEERKAIARFAIDHVDRRVPVLIGTGGTNARETIELSQHAQQAGADG
IVVINPYYWKVSEANLIRYFEQVADSVTLPVMLYNFPALTGQDLTPALVK
TLADSRSNIIGIKDTIDSVAHLRSMIHTVKGAHPHFTVLCGYDDHLFNTL
LLGGDGAISASGNFAPQVSVNLLKAWRDGDVAKAAGYHQTLLQIPQMYQL
DTPFVNVIKEAIVLCGRPVSTHVLPPASPLDEPRKAQLKTLLQQLKLC

3D structure

• PDB: 4ptn Crystal structure of YagE, a putative DHDPS-like protein from Escherichia coli K12.
• Chain: D
• Resolution: 1.99 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): S56 Y119 Y145 L150 K174 I219
• Catalytic site (residue number reindexed from 1): S45 Y108 Y134 L139 K163 I208
• Enzyme Commision number: 4.1.2.28: 2-dehydro-3-deoxy-D-pentonate aldolase.
  4.1.2.51: 2-dehydro-3-deoxy-D-gluconate aldolase.

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	GXV	D	K174 G202 Y203 S220 A221 F265	K163 G191 Y192 S209 A210 F254
BS02	MG	D	P20 G57	P9 G46
BS03	PYR	D	D262 P290 D292	D251 P279 D281

Gene Ontology

Molecular Function

• GO:0016829 lyase activity
• GO:0042802 identical protein binding
• GO:0047440 2-dehydro-3-deoxy-D-pentonate aldolase activity
• GO:0061677 2-dehydro-3-deoxy-D-gluconate aldolase activity

Biological Process

• GO:0046176 aldonic acid catabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:4ptn, PDBe:4ptn, PDBj:4ptn
• PDBsum: 4ptn
• PubMed: 18361457
• UniProt: P75682|YAGE_ECOLI Putative 2-dehydro-3-deoxy-D-gluconate aldolase YagE (Gene Name=yagE)