4DJD | pdb_00004djd

Crystal structure of folate-free corrinoid iron-sulfur protein (CFeSP) in complex with its methyltransferase (MeTr)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d4djda_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Dihydropteroate synthetase-like	Methyltetrahydrofolate-utiluzing methyltransferases	automated matches	(Neomoorella thermoacetica ) [TaxId: 1525 ],	SCOPe (2.08)
B	d4djdb_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Dihydropteroate synthetase-like	Methyltetrahydrofolate-utiluzing methyltransferases	automated matches	(Neomoorella thermoacetica ) [TaxId: 1525 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Dihydropteroate synthetase-like	8089873	3000643	SCOP2B (2022-06-29)
F	SCOP2 Family	CdhD-like	8051754	4007502	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	Dihydropteroate synthetase-like	8089873	3000643	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	AcsC Fe-S domain-like	8089862	3002395	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Dihydropteroate synthetase-like	8089870	3000643	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	AcsC C-terminal domain-like	8089872	3002396	SCOP2B (2022-06-29)
E	SCOP2 Family	AcsC Fe-S domain-like	8045246	4004371	SCOP2 (2022-06-29)
E	SCOP2 Family	CdhD-like	8051753	4007502	SCOP2 (2022-06-29)
E	SCOP2 Family	AcsC cobalamin-binding domain	8089871	4007687	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	AcsC Fe-S domain-like	8089862	3002395	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	Dihydropteroate synthetase-like	8089870	3000643	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	AcsC C-terminal domain-like	8089872	3002396	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	Dihydropteroate synthetase-like	8043870	3000643	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Dihydropteroate synthetase-like	8043870	3000643	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)
D	CdhD_N	e4djdD1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: CdhD_N	ECOD (1.6)
F	CdhD_N	e4djdF1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: CdhD_N	ECOD (1.6)
C	CdhD_N	e4djdC4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: CdhD_N	ECOD (1.6)
C	CdhD_C	e4djdC1	A: a/b three-layered sandwiches	X: B12 binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit (From Topology)	H: B12 binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit (From Topology)	T: B12 binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit	F: CdhD_C	ECOD (1.6)
C	FeS	e4djdC3	A: few secondary structure elements	X: Fe-S cluster binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit (From Topology)	H: Fe-S cluster binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit (From Topology)	T: Fe-S cluster binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit	F: FeS	ECOD (1.6)
E	CdhD_N	e4djdE4	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: CdhD_N	ECOD (1.6)
E	CdhD_C	e4djdE1	A: a/b three-layered sandwiches	X: B12 binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit (From Topology)	H: B12 binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit (From Topology)	T: B12 binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit	F: CdhD_C	ECOD (1.6)
E	FeS	e4djdE3	A: few secondary structure elements	X: Fe-S cluster binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit (From Topology)	H: Fe-S cluster binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit (From Topology)	T: Fe-S cluster binding domain in carbon monoxide dehydrogenase corrinoid/iron-sulfur protein gamma subunit	F: FeS	ECOD (1.6)
A	Pterin_bind	e4djdA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Pterin_bind	ECOD (1.6)
B	Pterin_bind	e4djdB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Pterin_bind	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.20.20.20	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Dihydropteroate synthase-like	CATH (4.3.0)
F	3.20.20.20	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Dihydropteroate synthase-like	CATH (4.3.0)
C	3.20.20.20	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Dihydropteroate synthase-like	CATH (4.3.0)
C	3.40.50.11600	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
E	3.20.20.20	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Dihydropteroate synthase-like	CATH (4.3.0)
E	3.40.50.11600	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
A	3.20.20.20	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Dihydropteroate synthase-like	CATH (4.3.0)
B	3.20.20.20	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Dihydropteroate synthase-like	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D, F	Corrinoid/iron-sulfur protein small subunit	vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding	small molecule metabolic process metabolic process cellular process one-carbon metabolic process carbon fixation	-
C, E	Corrinoid/iron-sulfur protein large subunit	vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding	nucleoside phosphate metabolic process catabolic process organophosphate catabolic process primary metabolic process purine-containing compound catabolic process nucleoside phosphate catabolic process acetyl-CoA metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound catabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process catabolic process organophosphate catabolic process primary metabolic process purine-containing compound catabolic process nucleoside phosphate catabolic process acetyl-CoA metabolic process nucleobase-containing compound catabolic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound catabolic process acyl-CoA metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process phosphorus metabolic process acetyl-CoA catabolic process carbon fixation	-
A, B	5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity vitamin binding cobalamin binding tetrapyrrole binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding methyltetrahydrofolate:corrinoid/iron-sulfur protein methyltransferase activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding methionine synthase activity S-methyltransferase activity	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 metabolic process cellular process small molecule metabolic process sulfur compound metabolic process folic acid-containing compound metabolic 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 metabolic process cellular process small molecule metabolic process sulfur compound metabolic process folic acid-containing compound metabolic process modified amino acid metabolic process tetrahydrofolate metabolic process pteridine-containing compound metabolic process carbon fixation methylation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D, F	IPR016041	CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel	Domain
D, F	IPR004486	CO dehydrogenase/acetyl-CoA synthase delta subunit	Family
D, F	IPR011005	Dihydropteroate synthase-like superfamily	Homologous Superfamily
D, F	IPR051069	Acetyl-CoA decarbonylase/synthase complex subunit	Family
C, E	IPR016218	Acetyl-CoA decarbonylase/synthase complex, gamma subunit	Family
C, E	IPR016041	CO dehydrogenase/acetyl-CoA synthase delta subunit, TIM barrel	Domain
C, E	IPR007202	4Fe-4S domain	Domain
C, E	IPR011005	Dihydropteroate synthase-like superfamily	Homologous Superfamily
C, E	IPR051069	Acetyl-CoA decarbonylase/synthase complex subunit	Family
A, B	IPR050554	Methionine Synthase/Corrinoid	Family
A, B	IPR011005	Dihydropteroate synthase-like superfamily	Homologous Superfamily
A, B	IPR000489	Pterin-binding domain	Domain

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.