Structure of PDB 2qgh Chain A

Receptor sequence

>2qghA (length=394) Species: 210 (Helicobacter pylori)

NYEELFQTHKTPFYLYDFDKIKQAFLNYKEAFKGRKSLICYALKANSNLS
ILSLLAHLESGADCVSIGEIQRALKAGIKPYRIVFSGVGKSAFEIEQALK
LNILFLNVESFMELKTIETIAQSLGIKARISIRINPNIDAKTHPYISTGL
KENKFGVGEKEALEMFLWAKKSAFLEPVSVHFHIGSQLLDLEPIIEASQK
VAKIAKSLIALGIDLRFFDVGGGIGVSYENEETIKLYDYAQGILNALQGL
DLTIICEPGRSIVAESGELITQVLYEKKNKRFVIVDAGMNDFLRPSLYHA
KHAIRVITPSEISPCDVVGPVCESSDTFLKDAHLPELEPGDKIAIEKVGA
YGSSMASQYNSRPKLLELALEDKIRVIRKREALEDLWRLEEEGL

3D structure

• PDB: 2qgh Crystal structure of diaminopimelate decarboxylase from Helicobacter pylori complexed with L-lysine
• Chain: A
• Resolution: 2.3 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): K46 H185 E259
• Catalytic site (residue number reindexed from 1): K44 H183 E257
• Enzyme Commision number: 4.1.1.20: diaminopimelate decarboxylase.

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	PLP	A	K46 D65 H185 S188 G224 G225 E259 P260 G261 R262 Y358	K44 D63 H183 S186 G222 G223 E257 P258 G259 R260 Y351
BS02	LYS	A	I148 R262 R298 Y302 Y358	I146 R260 R294 Y298 Y351

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008836 diaminopimelate decarboxylase activity
• GO:0016830 carbon-carbon lyase activity
• GO:0016831 carboxy-lyase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0009085 lysine biosynthetic process
• GO:0009089 lysine biosynthetic process via diaminopimelate

External links

• PDB: RCSB:2qgh, PDBe:2qgh, PDBj:2qgh
• PDBsum: 2qgh
• UniProt: B4XMC6|DCDA_HELPX Diaminopimelate decarboxylase (Gene Name=lysA)