1Q3N | pdb_00001q3n

Crystal structure of KDO8P synthase in its binary complex with substrate PEP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1q3na_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Aldolase	Class I DAHP synthetase	3-deoxy-D-manno-octulosonate 8-phosphate synthase (KDO8P synthase)	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Aldolase	8032655	3000445	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	DAHP_synth_1	e1q3nA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: DAHP_synth_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00793	DAHP synthetase I family (DAHP_synth_1)	DAHP synthetase I family	Members of this family catalyse the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar cat ...	Members of this family catalyse the first step in aromatic amino acid biosynthesis from chorismate. E-coli has three related synthetases, which are inhibited by different aromatic amino acids. This family also includes KDSA which has very similar catalytic activity but is involved in the first step of liposaccharide biosynthesis. The enzyme is also part of the shikimate pathway, EC:2.5.1.54.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	2-dehydro-3-deoxyphosphooctonate aldolase	3-deoxy-8-phosphooctulonate synthase activity transferase activity transferase activity, transferring alkyl or aryl (other than methyl) groups catalytic activity identical protein binding protein binding binding	monosaccharide metabolic process lipopolysaccharide biosynthetic process oxoacid metabolic process lipid biosynthetic process carbohydrate derivative metabolic process organic acid biosynthetic process organic acid metabolic process keto-3-deoxy-D-manno-octulosonic acid biosynthetic process carboxylic acid biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process small molecule metabolic process carbohydrate derivative biosynthetic process carbohydrate metabolic process monosaccharide metabolic process lipopolysaccharide biosynthetic process oxoacid metabolic process lipid biosynthetic process carbohydrate derivative metabolic process organic acid biosynthetic process organic acid metabolic process keto-3-deoxy-D-manno-octulosonic acid biosynthetic process carboxylic acid biosynthetic process lipopolysaccharide metabolic process polysaccharide metabolic process small molecule metabolic process carbohydrate derivative biosynthetic process carbohydrate metabolic process small molecule biosynthetic process polysaccharide biosynthetic process carbohydrate biosynthetic process liposaccharide metabolic process carboxylic acid metabolic process monosaccharide biosynthetic process primary metabolic process macromolecule biosynthetic process keto-3-deoxy-D-manno-octulosonic acid metabolic process biosynthetic process metabolic process cellular process macromolecule metabolic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR006269	3-deoxy-8-phosphooctulonate synthase	Family
A	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A	IPR006218	DAHP synthetase I/KDSA	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	3-deoxy-8-phosphooctulonate synthase M-CSA #614	3-deoxy-d-manno-s-octulosonate-8-phosphate synthase from Escherichia coli (KDO8P) is responsible for the synthesis of the named product from Phosphenol Pyruvate (PEP) and arabinose-5-phosphate (A5P). It thus plays a role in the synthesis of complex lipids for the gram negative bacterial cell wall, so is a possible target for antibiotics. It displays homology with many PEP utilising enzymes, particularly the metal dependent enzyme DAHP synthase which works by a similar mechanism where a single amino acid change of non-metallo KDO8P changes it to metallo-KDO8P.	Defined by 3 residues: ASN:A-26LYS:A-60ASP:A-250 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 2.5.1.55 (PDB Primary Data) Search M-CSA Motif + EC 2.5.1.55

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.