7CNR | pdb_00007cnr

Crystal structure of Thermococcus kodakaraensis aconitase X (apo-form)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	LeuD/IlvD-like	8103410	3000947	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	LeuD/IlvD-like	8103410	3000947	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	LeuD/IlvD-like	8103410	3000947	SCOP2B (2022-06-29)
B	SCOP2 Family	AF0055-like	8103409	4002545	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	LeuD/IlvD-like	8103410	3000947	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	DUF126	e7cnrH1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: DUF126	ECOD (1.6)
F	DUF126	e7cnrF1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: DUF126	ECOD (1.6)
D	DUF126	e7cnrD1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: DUF126	ECOD (1.6)
B	DUF126	e7cnrB1	A: a/b three-layered sandwiches	X: The swivelling beta/beta/alpha domains	H: The swivelling beta/beta/alpha domain (From Topology)	T: The swivelling beta/beta/alpha domain	F: DUF126	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF04412	Aconitase X (AcnX)	Aconitase X	-	Family
B, D, F, H	PF01989	Aconitase X swivel domain (AcnX_swivel_put)	Aconitase X swivel domain	This entry represents a domain centrally found in Phosphomevalonate dehydratase small subunit from Aeropyrum pernix (PMDh-S) and similar prokaryotic proteins previously annotated as aconitase X subunit 2, the swiveling domain subunit [1]. PMDh-S is a ...	This entry represents a domain centrally found in Phosphomevalonate dehydratase small subunit from Aeropyrum pernix (PMDh-S) and similar prokaryotic proteins previously annotated as aconitase X subunit 2, the swiveling domain subunit [1]. PMDh-S is a component of a hydro-lyase that catalyses the dehydration of mevalonate 5-phosphate (MVA5P) to form trans- anhydromevalonate 5-phosphate (tAHMP) [2-3]. It is involved in the archaea; mevalonate (MVA) pathway, which provides fundamental precursos for isoprenoid biosynthesis such as isopentenyl diphosphate (IPP) and dimenthylallyl diphosphate (DMAPP) [2,4]. This domain is also found at the N-terminal end of Cis-3-hydroxy-L-proline dehydratase from Agrobacterium fabrum (LhpI), which catalyses the dehydration of cis-3-hydroxy-L-proline (c3LHyp) to Delta1-pyrroline-2- carboxylate (Pyr2C) [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	DUF521 domain-containing protein	lyase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	biosynthetic process isoprenoid biosynthetic process lipid biosynthetic process primary metabolic process metabolic process cellular process lipid metabolic process isoprenoid metabolic process	-
B, D, F, H	UPF0107 protein TK1248	hydro-lyase activity lyase activity catalytic activity carbon-oxygen lyase activity	isopentenyl diphosphate biosynthetic process lipid biosynthetic process acetyl-CoA metabolic process phospholipid metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process small molecule metabolic process amide metabolic process phosphorus metabolic process nucleoside phosphate metabolic process isoprenoid biosynthetic process isopentenyl diphosphate biosynthetic process lipid biosynthetic process acetyl-CoA metabolic process phospholipid metabolic process nucleobase-containing compound metabolic process acyl-CoA metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process sulfur compound metabolic process small molecule metabolic process amide metabolic process phosphorus metabolic process nucleoside phosphate metabolic process isoprenoid biosynthetic process primary metabolic process phospholipid biosynthetic process purine-containing compound metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process metabolic process cellular process isopentenyl diphosphate biosynthetic process, mevalonate pathway lipid metabolic process isoprenoid metabolic process isopentenyl diphosphate metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR007506	Phosphomevalonate dehydratase large subunit-like domain	Domain
B, D, F, H	IPR002840	Phosphomevalonate dehydratase small subunit-like domain	Domain
B, D, F, H	IPR012016	Phosphomevalonate dehydratase small subunit-like	Family
B, D, F, H	IPR020794	Phosphomevalonate dehydratase small subunit	Family

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.