1RM0 | pdb_00001rm0

Crystal Structure of Myo-Inositol 1-Phosphate Synthase From Saccharomyces cerevisiae In Complex With NAD+ and 2-deoxy-D-glucitol 6-(E)-vinylhomophosphonate

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	d1rm0a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Myo-inositol 1-phosphate synthase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1rm0a2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Myo-inositol 1-phosphate synthase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1rm0b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, N-terminal domain	Myo-inositol 1-phosphate synthase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1rm0b2	Alpha and beta proteins (a+b)	FwdE/GAPDH domain-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	Dihydrodipicolinate reductase-like	Myo-inositol 1-phosphate synthase	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	GAPDH-like	8058136	3000043	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	GAPDH-like	8058136	3000043	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	Inos-1-P_synth	e1rm0A1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: Inos-1-P_synth	ECOD (1.6)
A	NAD_binding_5	e1rm0A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_5	ECOD (1.6)
B	Inos-1-P_synth	e1rm0B1	A: a+b two layers	X: FwdE/GAPDH domain-like	H: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain (From Topology)	T: Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	F: Inos-1-P_synth	ECOD (1.6)
B	NAD_binding_5	e1rm0B2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_5	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.30.360.10	Alpha Beta	2-Layer Sandwich	Dihydrodipicolinate Reductase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF07994	Myo-inositol-1-phosphate synthase (NAD_binding_5)	Myo-inositol-1-phosphate synthase	-	Family
A, B	PF01658	Myo-inositol-1-phosphate synthase (Inos-1-P_synth)	Myo-inositol-1-phosphate synthase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	myo-inositol-phosphate synthase	intramolecular lyase activity isomerase activity inositol-3-phosphate synthase activity catalytic activity	lipid biosynthetic process primary metabolic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process polyol metabolic process small molecule biosynthetic process lipid biosynthetic process primary metabolic process phospholipid biosynthetic process phospholipid metabolic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process phosphorus metabolic process lipid metabolic process polyol metabolic process small molecule biosynthetic process alcohol metabolic process inositol biosynthetic process inositol metabolic process polyol biosynthetic process alcohol biosynthetic process small molecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR013021	Myo-inositol-1-phosphate synthase, GAPDH-like	Domain
A, B	IPR002587	Myo-inositol-1-phosphate synthase	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	inositol-3-phosphate synthase M-CSA #331	Inositol-3-phosphate synthase catalyses the conversion of D-glucose 6-phosphate to 1L-myo-inositol-1-phosphate, the first committed step in the production of all inositol-containing compounds, including phospholipids, either directly or by salvage. It requires NAD+, which dehydrogenates the -CHOH- group to -CO- at C-5 of the glucose 6-phosphate, making C-6 into an active methylene, able to condense with the -CHO at C-1. Finally, the enzyme-bound NADH reconverts C-5 into the -CHOH- form.	Defined by 4 residues: ASP:A-320LYS:A-369LYS:A-412LYS:A-489 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 5.5.1.4 (PDB Primary Data) Search M-CSA Motif + EC 5.5.1.4

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.