1GOX

REFINED STRUCTURE OF SPINACH GLYCOLATE OXIDASE AT 2 ANGSTROMS RESOLUTION

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
Protein Modification Annotation
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	d1goxa_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	FMN-linked oxidoreductases	FMN-linked oxidoreductases	Glycolate oxidase	spinach (Spinacia oleracea ) [TaxId: 3562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	FMN-linked oxidoreductases	8058077	4000080	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-linked oxidoreductases	8058078	3000014	SCOP2 (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	IMPDH_1st_1	e1goxA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: IMPDH_1st_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.20.70	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Aldolase class I	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01070	FMN-dependent dehydrogenase (FMN_dh)	FMN-dependent dehydrogenase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	(S)-2-HYDROXY-ACID OXIDASE, PEROXISOMAL	binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors binding nucleotide binding FMN binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor oxidoreductase activity oxidoreductase activity, acting on CH-OH group of donors (S)-2-hydroxy-acid oxidase activity catalytic activity	biological process involved in interspecies interaction between organisms response to stimulus response to other organism response to external stimulus response to external biotic stimulus response to biotic stimulus oxidative photosynthetic carbon pathway metabolic process cellular process cellular metabolic compound salvage photorespiration	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle peroxisome microbody cytoplasm intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012133	Alpha-hydroxy acid dehydrogenase, FMN-dependent	Family
A	IPR008259	FMN-dependent alpha-hydroxy acid dehydrogenase, active site	Active Site
A	IPR013785	Aldolase-type TIM barrel	Homologous Superfamily
A	IPR037396	FMN hydroxy acid dehydrogenase domain	Domain
A	IPR000262	FMN-dependent dehydrogenase	Domain

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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

Chains	Enzyme Name	Description	Catalytic Residues
A	(S)-2-hydroxy-acid oxidase M-CSA #852	Glycolate oxidase is a flavoenzyme, which contains a permanently bound FNN cofactor. It catalyses the oxidation of (S)-2-hydroxy-acid to 2-oxo acid. In green plants, glycolate oxidase is one of the key enzymes in photorespiration where it oxidizes glycolate to glyoxylate. Comparison of properties with the extensively studied L-lactate oxidase and the topography of the active site and the amino acids surrounding the prosthetic group FMN led to the proposal of a reaction mechanism.	Defined by 5 residues: SER:A-107 [auth A-106]TYR:A-130 [auth A-129]THR:A-156 [auth A-155]LYS:A-231 [auth A-230]HIS:A-255 [auth A-254] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.1.3.1 (PDB Primary Data) Search M-CSA Motif + EC 1.1.3.1 EC: 1.1.3.15 (UniProt) Search M-CSA Motif + EC 1.1.3.15

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.