2NXH | pdb_00002nxh

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
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)
L	d2nxhl_	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	d2nxhk_	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	d2nxhj_	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	d2nxhi_	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	d2nxhh_	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	d2nxhg_	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	d2nxhf_	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	d2nxhe_	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	d2nxhd_	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	d2nxhc_	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	d2nxhb_	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)
A	d2nxha_	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)
L	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Aldolase	8036477	3000445	SCOP2B (2022-06-29)
A	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)
L	Biopterin_H	e2nxhL1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
K	Biopterin_H	e2nxhK1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
J	Biopterin_H	e2nxhJ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
I	Biopterin_H	e2nxhI1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
H	Biopterin_H	e2nxhH1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
G	Biopterin_H	e2nxhG1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
F	Biopterin_H	e2nxhF1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
E	Biopterin_H	e2nxhE1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
D	Biopterin_H	e2nxhD1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
C	Biopterin_H	e2nxhC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
B	Biopterin_H	e2nxhB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)
A	Biopterin_H	e2nxhA1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Biopterin_H	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	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)
J	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)
H	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)
F	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)
D	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)
B	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

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 biosynthetic process small molecule biosynthetic process carbohydrate biosynthetic process monosaccharide biosynthetic process small molecule metabolic process metabolic process cellular process primary metabolic process lipopolysaccharide biosynthetic process oxoacid metabolic process lipid biosynthetic process carbohydrate derivative metabolic process monosaccharide metabolic process carbohydrate metabolic process biosynthetic process small molecule biosynthetic process carbohydrate biosynthetic process monosaccharide biosynthetic process small molecule metabolic process metabolic process cellular process primary 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 carbohydrate derivative biosynthetic process polysaccharide biosynthetic process liposaccharide metabolic process carboxylic acid metabolic process macromolecule biosynthetic process macromolecule metabolic process lipid metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.