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 SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad1rm0a1 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)
Ad1rm0a2 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)
Bd1rm0b1 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)
Bd1rm0b2 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

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyGAPDH-like 8058136 3000043 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyGAPDH-like 8058136 3000043 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Ae1rm0A1 A: C-terminal subdomain in Lon-related proteases catalytic domainsX: C-terminal subdomain in Lon-related proteases catalytic domainsH: C-terminal subdomain in Lon-related proteases catalytic domainsT: NTP_transf_2, PAP_NTPaseF:ECOD (20:10:01)
Ae1rm0A2 A: C-terminal subdomain in Lon-related proteases catalytic domainsX: C-terminal subdomain in Lon-related proteases catalytic domainsH: C-terminal subdomain in Lon-related proteases catalytic domainsT: NAD_binding_3F:ECOD (20:10:01)
Be1rm0B1 A: C-terminal subdomain in Lon-related proteases catalytic domainsX: C-terminal subdomain in Lon-related proteases catalytic domainsH: C-terminal subdomain in Lon-related proteases catalytic domainsT: NTP_transf_2, PAP_NTPaseF:ECOD (20:10:01)
Be1rm0B2 A: C-terminal subdomain in Lon-related proteases catalytic domainsX: C-terminal subdomain in Lon-related proteases catalytic domainsH: C-terminal subdomain in Lon-related proteases catalytic domainsT: NAD_binding_3F:ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
A3.30.360.10 Alpha Beta 2-Layer Sandwich Dihydrodipicolinate Reductase domain 2CATH (4.3.0)
B3.40.50.720 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NAD(P)-binding Rossmann-like DomainCATH (4.3.0)
B3.30.360.10 Alpha Beta 2-Layer Sandwich Dihydrodipicolinate Reductase domain 2CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF07994Myo-inositol-1-phosphate synthase (NAD_binding_5)Myo-inositol-1-phosphate synthase- Family
A, B
PF01658Myo-inositol-1-phosphate synthase (Inos-1-P_synth)Myo-inositol-1-phosphate synthase- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
myo-inositol-phosphate synthase

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B
IPR036291NAD(P)-binding domain superfamilyHomologous Superfamily
A, B
IPR013021Myo-inositol-1-phosphate synthase, GAPDH-likeDomain
A, B
IPR002587Myo-inositol-1-phosphate synthaseFamily

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

ChainsEnzyme NameDescriptionCatalytic Residues
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
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Explore in 3D: M-CSA Motif Definition
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EC: 5.5.1.4 (PDB Primary Data)