1IK4 | pdb_00001ik4

X-ray Structure of Methylglyoxal Synthase from E. coli Complexed with Phosphoglycolohydroxamic Acid

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	d1ik4a_	Alpha and beta proteins (a/b)	Methylglyoxal synthase-like	Methylglyoxal synthase-like	Methylglyoxal synthase, MgsA	Methylglyoxal synthase, MgsA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d1ik4b_	Alpha and beta proteins (a/b)	Methylglyoxal synthase-like	Methylglyoxal synthase-like	Methylglyoxal synthase, MgsA	Methylglyoxal synthase, MgsA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d1ik4c_	Alpha and beta proteins (a/b)	Methylglyoxal synthase-like	Methylglyoxal synthase-like	Methylglyoxal synthase, MgsA	Methylglyoxal synthase, MgsA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d1ik4d_	Alpha and beta proteins (a/b)	Methylglyoxal synthase-like	Methylglyoxal synthase-like	Methylglyoxal synthase, MgsA	Methylglyoxal synthase, MgsA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d1ik4e_	Alpha and beta proteins (a/b)	Methylglyoxal synthase-like	Methylglyoxal synthase-like	Methylglyoxal synthase, MgsA	Methylglyoxal synthase, MgsA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d1ik4f_	Alpha and beta proteins (a/b)	Methylglyoxal synthase-like	Methylglyoxal synthase-like	Methylglyoxal synthase, MgsA	Methylglyoxal synthase, MgsA	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Methylglyoxal synthase-like	8044173	3001443	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Methylglyoxal synthase-like	8044173	3001443	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Methylglyoxal synthase-like	8044173	3001443	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Methylglyoxal synthase-like	8044173	3001443	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Methylglyoxal synthase-like	8044173	3001443	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Methylglyoxal synthase-like	8044173	3001443	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	MGS	e1ik4A1	A: a/b three-layered sandwiches	X: Methylglyoxal synthase-like (From Topology)	H: Methylglyoxal synthase-like (From Topology)	T: Methylglyoxal synthase-like	F: MGS	ECOD (1.6)
B	MGS	e1ik4B1	A: a/b three-layered sandwiches	X: Methylglyoxal synthase-like (From Topology)	H: Methylglyoxal synthase-like (From Topology)	T: Methylglyoxal synthase-like	F: MGS	ECOD (1.6)
C	MGS	e1ik4C1	A: a/b three-layered sandwiches	X: Methylglyoxal synthase-like (From Topology)	H: Methylglyoxal synthase-like (From Topology)	T: Methylglyoxal synthase-like	F: MGS	ECOD (1.6)
D	MGS	e1ik4D1	A: a/b three-layered sandwiches	X: Methylglyoxal synthase-like (From Topology)	H: Methylglyoxal synthase-like (From Topology)	T: Methylglyoxal synthase-like	F: MGS	ECOD (1.6)
E	MGS	e1ik4E1	A: a/b three-layered sandwiches	X: Methylglyoxal synthase-like (From Topology)	H: Methylglyoxal synthase-like (From Topology)	T: Methylglyoxal synthase-like	F: MGS	ECOD (1.6)
F	MGS	e1ik4F1	A: a/b three-layered sandwiches	X: Methylglyoxal synthase-like (From Topology)	H: Methylglyoxal synthase-like (From Topology)	T: Methylglyoxal synthase-like	F: MGS	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylglyoxal synthase-like domain	CATH (4.3.0)
B	3.40.50.1380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylglyoxal synthase-like domain	CATH (4.3.0)
C	3.40.50.1380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylglyoxal synthase-like domain	CATH (4.3.0)
D	3.40.50.1380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylglyoxal synthase-like domain	CATH (4.3.0)
E	3.40.50.1380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylglyoxal synthase-like domain	CATH (4.3.0)
F	3.40.50.1380	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylglyoxal synthase-like domain	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	PF02142	MGS-like domain (MGS)	MGS-like domain	This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes ino ...	This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site [1].	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	METHYLGLYOXAL SYNTHASE	carbon-oxygen lyase activity, acting on phosphates lyase activity methylglyoxal synthase activity catalytic activity carbon-oxygen lyase activity identical protein binding protein binding binding	methylglyoxal biosynthetic process small molecule biosynthetic process ketone metabolic process aldehyde biosynthetic process aldehyde metabolic process biosynthetic process metabolic process cellular process small molecule metabolic process ketone biosynthetic process methylglyoxal metabolic process cellular component organization cellular component biogenesis protein hexamerization methylglyoxal biosynthetic process small molecule biosynthetic process ketone metabolic process aldehyde biosynthetic process aldehyde metabolic process biosynthetic process metabolic process cellular process small molecule metabolic process ketone biosynthetic process methylglyoxal metabolic process cellular component organization cellular component biogenesis protein hexamerization cellular component assembly protein-containing complex organization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis	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	IPR018148	Methylglyoxal synthase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F	IPR004363	Methylglyoxal synthase	Family
A, B, C, D, E A, B, C, D, E, F	IPR011607	Methylglyoxal synthase-like domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036914	Methylglyoxal synthase-like domain superfamily	Homologous Superfamily

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.