2NX3

Structural and mechanistic changes along an engineered path from metallo to non-metallo KDO8P synthase

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2nx3a_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
B	d2nx3b_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
C	d2nx3c_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
D	d2nx3d_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
E	d2nx3e_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
F	d2nx3f_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
G	d2nx3g_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
H	d2nx3h_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
I	d2nx3i_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
J	d2nx3j_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
K	d2nx3k_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	SCOPe (2.08)
L	d2nx3l_	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)	(Aquifex aeolicus ) [TaxId: 63363 ],	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	8036477	3000445	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Aldolase	8036477	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	PF00793	e2nx3A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
B	PF00793	e2nx3B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
C	PF00793	e2nx3C1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
D	PF00793	e2nx3D1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
E	PF00793	e2nx3E1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
F	PF00793	e2nx3F1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
G	PF00793	e2nx3G1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
H	PF00793	e2nx3H1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
I	PF00793	e2nx3I1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
J	PF00793	e2nx3J1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
K	PF00793	e2nx3K1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	ECOD (1.6)
L	PF00793	e2nx3L1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00793	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)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
C	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
D	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
E	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
F	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
G	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
H	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
I	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
J	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
K	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
L	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, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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	monosaccharide metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process monosaccharide biosynthetic process primary metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process small molecule metabolic process metabolic process lipopolysaccharide biosynthetic process oxoacid metabolic process cellular biosynthetic process monosaccharide metabolic process carbohydrate metabolic process small molecule biosynthetic process carbohydrate biosynthetic process monosaccharide biosynthetic process primary metabolic process organic substance metabolic process biosynthetic process organic substance biosynthetic process small molecule metabolic process metabolic process lipopolysaccharide biosynthetic process oxoacid metabolic process cellular biosynthetic 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 carbohydrate derivative biosynthetic process polysaccharide biosynthetic process cellular metabolic process liposaccharide metabolic process carboxylic acid metabolic process macromolecule biosynthetic process keto-3-deoxy-D-manno-octulosonic acid metabolic process cellular process macromolecule metabolic process lipid metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006269	3-deoxy-8-phosphooctulonate synthase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR006218	DAHP synthetase I/KDSA	Domain

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 R01GM133198.