1DL5 | pdb_00001dl5

PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE

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	d1dl5a1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Protein-L-isoaspartyl O-methyltransferase	Protein-L-isoaspartyl O-methyltransferase	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
A	d1dl5a2	Alpha and beta proteins (a+b)	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1dl5b1	Alpha and beta proteins (a/b)	S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	Protein-L-isoaspartyl O-methyltransferase	Protein-L-isoaspartyl O-methyltransferase	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)
B	d1dl5b2	Alpha and beta proteins (a+b)	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	(Thermotoga maritima ) [TaxId: 2336 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Protein-L-isoaspartyl O-methyltransferase	8023071	4000666	SCOP2 (2022-06-29)
A	SCOP2 Family	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	8023074	4002824	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8035451	3000118	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	8035454	3001797	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	S-adenosyl-L-methionine-dependent methyltransferases	8035451	3000118	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	8035454	3001797	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	PIMT_C	e1dl5A1	A: a+b two layers	X: TBP-like	H: Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	T: Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	F: PIMT_C	ECOD (develop294)
A	PCMT, Methyltransf_31	e1dl5A2	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PCMT, Methyltransf_31	ECOD (develop294)
B	Glyco_hydro_18	e1dl5B1	A: alpha bundles	X: EGF-like	H: LDL receptor-like module	T: LDL receptor-like module	F: Glyco_hydro_18	ECOD (develop294)
B	PCMT, Methyltransf_25	e1dl5B2	A: alpha bundles	X: HTH	H: HTH	T: winged helix domain	F: PCMT, Methyltransf_25	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
A	3.55.20.10	Alpha Beta	3-Layer(bab) Sandwich	Protein-l-isoaspartate O-methyltransferase	Chain: A, domain 2	CATH (4.3.0)
B	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
B	3.55.20.10	Alpha Beta	3-Layer(bab) Sandwich	Protein-l-isoaspartate O-methyltransferase	Chain: A, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01135	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) (PCMT)	Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT)	-	Family
A, B	PF20799	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain (PIMT_C)	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	Protein-L-isoaspartyl O-methyltransferase (PIMT) from Thermotoga maritima is a conserved and nearly ubiquitous enzyme involved in the repair of proteins damaged by age-related isoaspartyl formation. PIMT consists of three domains. This entry represen ...	Protein-L-isoaspartyl O-methyltransferase (PIMT) from Thermotoga maritima is a conserved and nearly ubiquitous enzyme involved in the repair of proteins damaged by age-related isoaspartyl formation. PIMT consists of three domains. This entry represents its C-terminal domain, which shows a five-stranded beta meander flanked on both sides by alpha helices. Its function is unknown [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PROTEIN-L-ISOASPARTATE O-METHYLTRANSFERASE	O-methyltransferase activity catalytic activity, acting on a protein protein-L-isoaspartate (D-aspartate) O-methyltransferase activity transferase activity, transferring one-carbon groups transferase activity S-adenosylmethionine-dependent methyltransferase activity carboxyl-O-methyltransferase activity protein carboxyl O-methyltransferase activity protein methyltransferase activity methyltransferase activity catalytic activity	methylation metabolic process cellular process protein repair primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR049284	Protein-L-isoaspartyl O-methyltransferase, C-terminal domain	Domain
A, B	IPR009107	Protein-L-isoaspartyl O-methyltransferase, C-terminal	Homologous Superfamily
A, B	IPR000682	Protein-L-isoaspartate(D-aspartate) O-methyltransferase	Family
A, B	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily

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

Chains	Enzyme Name	Description	Catalytic Residues
A	protein-L-isoaspartate(D-aspartate) O-methyltransferase M-CSA #692	Formation of isoaspartyl residues is one of several processes that damage proteins as they age. Protein L-isoaspartate (D-aspartate) O-methyltransferase (PIMT) is a conserved and nearly ubiquitous enzyme that catalyzes the repair of proteins damaged by isoaspartyl formation.	Defined by 1 residue: SER:A-59 \| Explore in 3D: M-CSA Motif Definition At least 2 residues must be present to support Structure Motif searching. EC: 2.1.1.77 (PDB Primary Data)

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.