2O2K | pdb_00002o2k

Crystal Structure of the Activation Domain of Human Methionine Synthase Isoform/Mutant D963E/K1071N

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2o2ka_	Alpha and beta proteins (a+b)	Methionine synthase activation domain-like	Methionine synthase activation domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d2o2kb_	Alpha and beta proteins (a+b)	Methionine synthase activation domain-like	Methionine synthase activation domain-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Methionine synthase SAM-binding domain	8077296	4002546	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Methionine synthase activation domain-like	8077297	3001398	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Methionine synthase activation domain-like	8077297	3001398	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	Met_synt_B12	e2o2kA1	A: a+b complex topology	X: Methionine synthase activation domain-like (From Topology)	H: Methionine synthase activation domain-like (From Topology)	T: Methionine synthase activation domain-like	F: Met_synt_B12	ECOD (1.6)
B	Met_synt_B12	e2o2kB1	A: a+b complex topology	X: Methionine synthase activation domain-like (From Topology)	H: Methionine synthase activation domain-like (From Topology)	T: Methionine synthase activation domain-like	F: Met_synt_B12	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.196.10	Alpha Beta	Roll	Cobalamin-dependent Methionine Synthase	domain 1	CATH (4.3.0)
A	1.10.288.10	Mainly Alpha	Orthogonal Bundle	Cobalamin-dependent Methionine Synthase	domain 2	CATH (4.3.0)
B	3.10.196.10	Alpha Beta	Roll	Cobalamin-dependent Methionine Synthase	domain 1	CATH (4.3.0)
B	1.10.288.10	Mainly Alpha	Orthogonal Bundle	Cobalamin-dependent Methionine Synthase	domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02965	Vitamin B12 dependent methionine synthase, activation domain (Met_synt_B12)	Vitamin B12 dependent methionine synthase, activation domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Methionine synthase	vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding methionine synthase activity 5-methyltetrahydrofolate-dependent methyltransferase activity transferase activity, transferring one-carbon groups S-methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding methionine synthase activity 5-methyltetrahydrofolate-dependent methyltransferase activity transferase activity, transferring one-carbon groups S-methyltransferase activity transferase activity methyltransferase activity catalytic activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	response to stimulus response to stress response to wounding response to axon injury methylation metabolic process cellular process homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process response to stimulus response to stress response to wounding response to axon injury methylation metabolic process cellular process homocysteine metabolic process oxoacid metabolic process sulfur amino acid metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process small molecule metabolic process sulfur compound metabolic process cobalamin metabolic process tetrapyrrole metabolic process water-soluble vitamin metabolic process vitamin metabolic process aspartate family amino acid biosynthetic process aspartate family amino acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process methionine biosynthetic process small molecule biosynthetic process L-amino acid biosynthetic process methionine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process folic acid-containing compound metabolic process modified amino acid metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process developmental process multicellular organism development multicellular organismal process anatomical structure development nervous system development system development cellular response to stimulus cellular developmental process cell projection organization cell development neuron projection development regeneration neuron projection regeneration cellular component organization neurogenesis axon regeneration neuron differentiation cellular response to stress cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization axon development generation of neurons neuron development cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to nitric oxide cellular response to chemical stimulus response to chemical response to nitric oxide cellular response to reactive nitrogen species	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003759	Cobalamin (vitamin B12)-binding module, cap domain	Domain
A, B	IPR006158	Cobalamin (vitamin B12)-binding domain	Domain
A, B	IPR003726	Homocysteine-binding domain	Domain
A, B	IPR004223	Vitamin B12-dependent methionine synthase, activation domain	Domain
A, B	IPR000489	Pterin-binding domain	Domain
A, B	IPR036724	Cobalamin-binding domain superfamily	Homologous Superfamily
A, B	IPR036594	Methionine synthase domain	Homologous Superfamily
A, B	IPR037010	Vitamin B12-dependent methionine synthase, activation domain superfamily	Homologous Superfamily
A, B	IPR050554	Methionine Synthase/Corrinoid	Family
A, B	IPR011005	Dihydropteroate synthase-like superfamily	Homologous Superfamily
A, B	IPR033706	Methionine synthase, B12-binding domain	Domain
A, B	IPR036589	Homocysteine-binding domain superfamily	Homologous Superfamily
A, B	IPR011822	Cobalamin-dependent methionine synthase	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: Q99707	follicular lymphoma neural tube defects, folate-sensitive homocystinuria cleft palate hematologic disease lymphoma Down syndrome methylcobalamin deficiency type cblG Leukoencephalopathies male infertility breast carcinoma ovarian cancer progressive supranuclear palsy hyperhomocysteinemia intellectual disability follicular lymphoma neural tube defects, folate-sensitive homocystinuria cleft palate hematologic disease lymphoma Down syndrome methylcobalamin deficiency type cblG Leukoencephalopathies male infertility breast carcinoma ovarian cancer progressive supranuclear palsy hyperhomocysteinemia intellectual disability bipolar disorder myopathy peripheral nervous system disease psoriasis inborn errors of metabolism breast cancer cleft lip depressive disorder medulloblastoma neural tube defect osteosarcoma peripheral neuropathy schizophrenia inborn vitamin B12 deficiency tethered spinal cord syndrome leukoencephalopathy with vanishing white matter attention deficit hyperactivity disorder, inattentive type congenital anemia digestive system disease methylmalonic acidemia

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.