1XA8 | pdb_00001xa8

Crystal Structure Analysis of Glutathione-dependent formaldehyde-activating enzyme (Gfa)

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	d1xa8a1	All beta proteins	Mss4-like	Mss4-like	Glutathione-dependent formaldehyde-activating enzyme, Gfa	Glutathione-dependent formaldehyde-activating enzyme, Gfa	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
A	d1xa8a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B	d1xa8b1	All beta proteins	Mss4-like	Mss4-like	Glutathione-dependent formaldehyde-activating enzyme, Gfa	Glutathione-dependent formaldehyde-activating enzyme, Gfa	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
B	d1xa8b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
C	d1xa8c1	All beta proteins	Mss4-like	Mss4-like	Glutathione-dependent formaldehyde-activating enzyme, Gfa	Glutathione-dependent formaldehyde-activating enzyme, Gfa	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
C	d1xa8c2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
D	d1xa8d1	All beta proteins	Mss4-like	Mss4-like	Glutathione-dependent formaldehyde-activating enzyme, Gfa	Glutathione-dependent formaldehyde-activating enzyme, Gfa	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)
D	d1xa8d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Paracoccus denitrificans ) [TaxId: 266 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Mss4-like	8043736	3001994	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Mss4-like	8043736	3001994	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Mss4-like	8043736	3001994	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Mss4-like	8043736	3001994	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	GFA	e1xa8A1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: GFA	ECOD (1.6)
B	GFA	e1xa8B1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: GFA	ECOD (1.6)
C	GFA	e1xa8C1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: GFA	ECOD (1.6)
D	GFA	e1xa8D1	A: beta complex topology	X: ETN0001 domain-like (From Homology)	H: ETN0001 domain-like	T: Mss4-like	F: GFA	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1590.10	Alpha Beta	Alpha-Beta Complex	glutathione-dependent formaldehyde- activating enzyme (gfa)	glutathione-dependent formaldehyde- activating enzyme (gfa)	CATH (4.3.0)
B	3.90.1590.10	Alpha Beta	Alpha-Beta Complex	glutathione-dependent formaldehyde- activating enzyme (gfa)	glutathione-dependent formaldehyde- activating enzyme (gfa)	CATH (4.3.0)
C	3.90.1590.10	Alpha Beta	Alpha-Beta Complex	glutathione-dependent formaldehyde- activating enzyme (gfa)	glutathione-dependent formaldehyde- activating enzyme (gfa)	CATH (4.3.0)
D	3.90.1590.10	Alpha Beta	Alpha-Beta Complex	glutathione-dependent formaldehyde- activating enzyme (gfa)	glutathione-dependent formaldehyde- activating enzyme (gfa)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF04828	Glutathione-dependent formaldehyde-activating enzyme (GFA)	Glutathione-dependent formaldehyde-activating enzyme	The GFA enzyme catalyzes the first step in the detoxification of formaldehyde. This domain has a beta-tent fold [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glutathione-dependent formaldehyde-activating enzyme	carbon-sulfur lyase activity lyase activity catalytic activity S-(hydroxymethyl)glutathione synthase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	cellular response to stimulus cellular detoxification catabolic process response to stimulus formaldehyde catabolic process detoxification response to oxygen-containing compound cellular response to oxygen-containing compound aldehyde metabolic process response to toxic substance cellular detoxification of aldehyde cellular response to chemical stimulus cellular response to aldehyde response to chemical cellular response to stimulus cellular detoxification catabolic process response to stimulus formaldehyde catabolic process detoxification response to oxygen-containing compound cellular response to oxygen-containing compound aldehyde metabolic process response to toxic substance cellular detoxification of aldehyde cellular response to chemical stimulus cellular response to aldehyde response to chemical metabolic process cellular process small molecule metabolic process formaldehyde metabolic process aldehyde catabolic process small molecule catabolic process cellular response to toxic substance	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR006913	CENP-V/GFA domain	Domain
A, B, C, D	IPR011057	Mss4-like superfamily	Homologous Superfamily
A, B, C, D	IPR014185	Glutathione-dependent formaldehyde-activating enzyme	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	S-(hydroxymethyl)glutathione synthase M-CSA #712	Glutathione-dependent formaldehyde-activating enzyme (Gfa) is a carbon-sulphur lyase enzyme that catalyses the first step of a pathway that metabolises toxic formaldehyde to yield formate as a product. Gfa catalyses the condensation of formaledhyde and glutathione to form an adduct, S-hydroxymethylglutathione.	Defined by 3 residues: CYS:A-54CYS:A-56CYS:A-59 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 4.4 (PDB Primary Data) Search M-CSA Motif + EC 4.4 EC: 4.4.1.22 (UniProt) Search M-CSA Motif + EC 4.4.1.22

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.