Structure of PDB 2d2x Chain A

Receptor sequence

>2d2xA (length=353) Species: 1397 (Niallia circulans)

TTKQICFADRCFNFAFGEHVLESVESYIPRDEFDQYIMISDSGVPDSIVH
YAAEYFGKLAPVHILRFQGGEEYKTLSTVTNLQERAIALGANRRTAIVAV
GGGLTGNVAGVAAGMMFRGIALIHVPTTFLAASDSVLSIKQAVNLTSGKN
LVGFYYPPRFVFADTRILSESPPRQVKAGMCELVKNMLILKEFTEDDLNS
ANVYSPKQLETFINFCISAKMSVLSEDIYEKKKGLIFEYGHTIGHAIELA
EQGGITHGEAIAVGMIYAAKIANRMNLMPEHDVSAHYWLLNKIGALQDIP
LKSDPDSIFHYLIHEDNLGMILLSGVGKPAMYNQTLLTPVRKTLIKEVIR
EGL

3D structure

• PDB: 2d2x Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+
• Chain: A
• Resolution: 2.3 Å

Enzymatic activity

• Catalytic site (original residue number in PDB): R119 K141 E183 K225 E235 G239 E243 H246 H250 H262
• Catalytic site (residue number reindexed from 1): R118 K140 E182 K220 E230 G234 E238 H241 H245 H257
• Enzyme Commision number: 4.2.3.124: 2-deoxy-scyllo-inosose synthase.

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	CO	A	E183 H246 H262	E182 H241 H257
BS02	CO	A	D42 G103 L105 T106	D41 G102 L104 T105
BS03	CO	A	E235 G239 E243	E230 G234 E238
BS04	SO3	A	Y244 G245 T247 M335 I336	Y239 G240 T242 M320 I321

Gene Ontology

Molecular Function

• GO:0003856 3-dehydroquinate synthase activity
• GO:0016829 lyase activity
• GO:0016838 carbon-oxygen lyase activity, acting on phosphates
• GO:0046872 metal ion binding

Biological Process

• GO:0009073 aromatic amino acid family biosynthetic process
• GO:0017000 antibiotic biosynthetic process

External links

• PDB: RCSB:2d2x, PDBe:2d2x, PDBj:2d2x
• PDBsum: 2d2x
• PubMed: 17879343
• UniProt: Q9S5E2|DOIS_NIACI 2-deoxy-scyllo-inosose synthase (Gene Name=btrC)