3R9A

Human alanine-glyoxylate aminotransferase in complex with the TPR domain of human PEX5P

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
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3r9aa_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3r9ac_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	Cystathionine synthase-like	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3r9ab_	All alpha proteins	alpha-alpha superhelix	TPR-like	Tetratricopeptide repeat (TPR)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3r9ad_	All alpha proteins	alpha-alpha superhelix	TPR-like	Tetratricopeptide repeat (TPR)	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	SCOP2B Superfamily	PLP-dependent transferases	8044494	3000954	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8044494	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TPR-like	8038651	3001345	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	TPR-like	8038651	3001345	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	AGAT_like	e3r9aA3	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: AGAT_like	ECOD (1.6)
A	Aminotran_5_N	e3r9aA2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
C	AGAT_like	e3r9aC3	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: AGAT_like	ECOD (1.6)
C	Aminotran_5_N	e3r9aC2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
B	TPR_15	e3r9aB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TPR_15	ECOD (1.6)
D	TPR_15	e3r9aD1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TPR_15	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
A	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
C	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)
D	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00266	Aminotransferase class-V (Aminotran_5)	Aminotransferase class-V	This domain is found in amino transferases, and other enzymes including cysteine desulphurase EC:4.4.1.-.	Domain
B, D	PF13181	Tetratricopeptide repeat (TPR_8)	Tetratricopeptide repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Serine--pyruvate aminotransferase	transferase activity, transferring nitrogenous groups transaminase activity transferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding serine-pyruvate transaminase activity transferase activity, transferring nitrogenous groups transaminase activity transferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding serine-pyruvate transaminase activity alanine-glyoxylate transaminase activity amino acid binding identical protein binding protein binding protein homodimerization activity protein dimerization activity	serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glycine metabolic process glycine biosynthetic process organic substance metabolic process glycine biosynthetic process, by transamination of glyoxylate organic substance biosynthetic process serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glycine metabolic process glycine biosynthetic process organic substance metabolic process glycine biosynthetic process, by transamination of glyoxylate organic substance biosynthetic process small molecule metabolic process organonitrogen compound metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process catabolic process L-cysteine catabolic process sulfur amino acid metabolic process L-cysteine metabolic process organic acid catabolic process cellular catabolic process carboxylic acid catabolic process sulfur compound metabolic process amino acid catabolic process organonitrogen compound catabolic process L-amino acid catabolic process cysteine metabolic process serine family amino acid catabolic process sulfur compound catabolic process alpha-amino acid catabolic process proteinogenic amino acid catabolic process sulfur amino acid catabolic process cysteine catabolic process small molecule catabolic process organic substance catabolic process oxalic acid secretion organic anion transport carboxylic acid transport secretion transport organic substance transport acid secretion establishment of localization organic acid transport localization oxalate transport dicarboxylic acid transport glyoxylate metabolic process cellular aldehyde metabolic process monocarboxylic acid metabolic process pyruvate family amino acid metabolic process alanine catabolic process pyruvate family amino acid catabolic process L-alanine catabolic process L-alanine metabolic process alanine metabolic process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication Notch signaling pathway signal transduction L-serine metabolic process monocarboxylic acid catabolic process glyoxylate catabolic process aldehyde catabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle peroxisome microbody peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle intracellular organelle organelle intracellular membrane-bounded organelle peroxisome microbody peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen
B, D	Peroxisomal targeting signal 1 receptor	peroxisome matrix targeting signal-1 binding signal sequence binding binding peroxisome targeting sequence binding peptide binding small GTPase binding protein binding enzyme binding GTPase binding peroxisome membrane targeting sequence binding protein carrier chaperone molecular carrier activity	protein localization cellular localization establishment of protein localization protein localization to peroxisome nitrogen compound transport transport peroxisomal membrane transport cellular component organization localization peroxisome organization establishment of localization in cell cellular macromolecule localization cellular component organization or biogenesis establishment of protein localization to peroxisome protein localization cellular localization establishment of protein localization protein localization to peroxisome nitrogen compound transport transport peroxisomal membrane transport cellular component organization localization peroxisome organization establishment of localization in cell cellular macromolecule localization cellular component organization or biogenesis establishment of protein localization to peroxisome protein import into peroxisome membrane establishment of protein localization to membrane organic substance transport intracellular transport localization within membrane protein localization to membrane establishment of localization peroxisomal transport organelle organization establishment of protein localization to organelle protein transport macromolecule localization protein localization to organelle cellular process intracellular protein transport cellular component biogenesis cellular component assembly protein-containing complex organization protein complex oligomerization protein tetramerization protein-containing complex assembly developmental process multicellular organismal process head development cellular developmental process forebrain development animal organ development brain development nervous system development generation of neurons multicellular organism development central nervous system neuron differentiation neurogenesis central nervous system development neuron differentiation cell differentiation anatomical structure development cerebral cortex neuron differentiation system development catabolic process oxoacid metabolic process organic acid catabolic process organic acid metabolic process cellular lipid catabolic process cellular catabolic process organic substance metabolic process monocarboxylic acid catabolic process fatty acid oxidation carboxylic acid catabolic process fatty acid beta-oxidation small molecule metabolic process lipid oxidation fatty acid metabolic process lipid catabolic process cellular metabolic process carboxylic acid metabolic process primary metabolic process lipid modification fatty acid catabolic process cellular lipid metabolic process metabolic process monocarboxylic acid metabolic process small molecule catabolic process organic substance catabolic process lipid metabolic process cell development protein transmembrane import into intracellular organelle protein import into peroxisome matrix, translocation protein transmembrane transport intracellular protein transmembrane transport protein import into peroxisome matrix transmembrane transport cerebral cortex cell migration pallium development cerebral cortex development telencephalon cell migration forebrain cell migration cell migration telencephalon development cell motility regulation of biological process regulation of cellular process regulation of cellular component organization negative regulation of cellular component organization biological regulation negative regulation of biological process regulation of cellular component biogenesis negative regulation of protein-containing complex assembly regulation of protein-containing complex assembly negative regulation of cellular process autophagy of peroxisome macroautophagy pexophagy autophagy process utilizing autophagic mechanism system process nervous system process neuromuscular process protein targeting to peroxisome protein targeting endoplasmic reticulum organization endomembrane system organization protein-containing complex disassembly protein import into peroxisome matrix, substrate release cellular component disassembly cellular response to stimulus response to stimulus cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound response to reactive oxygen species cellular response to reactive oxygen species response to oxidative stress cellular response to chemical stimulus cellular response to stress response to stress response to chemical receptor metabolic process protein import into peroxisome matrix, receptor recycling receptor recycling macromolecule metabolic process mitochondrial membrane organization membrane organization mitochondrion organization regulation of multicellular organism growth regulation of growth regulation of developmental growth regulation of developmental process developmental growth growth positive regulation of biological process positive regulation of multicellular organism growth positive regulation of developmental process multicellular organism growth positive regulation of growth positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of developmental growth very long-chain fatty acid metabolic process neuron migration protein import into peroxisome matrix, docking	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane cytosol protein-containing complex Golgi apparatus endomembrane system peroxisome membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle membrane cytosol protein-containing complex Golgi apparatus endomembrane system peroxisome microbody microbody membrane bounding membrane of organelle peroxisomal membrane organelle membrane peroxisomal matrix membrane-enclosed lumen intracellular organelle lumen organelle lumen microbody lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR020578	Aminotransferase class-V, pyridoxal-phosphate binding site	Binding Site
A, C	IPR000192	Aminotransferase class V domain	Domain
A, C	IPR024169	Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase	Family
A, C	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, C	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, C	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
B, D	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
B, D	IPR019734	Tetratricopeptide repeat	Repeat
B, D	IPR024111	PEX5/PEX5L	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P21549	primary hyperoxaluria type 1 primary hyperoxaluria inborn errors of metabolism nephrolithiasis urolithiasis intellectual disability pancreatic ductal adenocarcinoma nephrocalcinosis peroxisomal disease primary hyperoxaluria type 2
B, D	Pharos: P50542	Zellweger spectrum disorders rhizomelic chondrodysplasia punctata type 5 peroxisome biogenesis disorder 2A (Zellweger) peroxisome biogenesis disorder 2B peroxisomal disease rhizomelic chondrodysplasia punctata peroxisome biogenesis disorder type 3B Adrenoleukodystrophy, Neonatal cataract diabetes mellitus adult Refsum disease cholestasis hydrops fetalis intellectual disability arthrogryposis Zellweger spectrum disorders rhizomelic chondrodysplasia punctata type 5 peroxisome biogenesis disorder 2A (Zellweger) peroxisome biogenesis disorder 2B peroxisomal disease rhizomelic chondrodysplasia punctata peroxisome biogenesis disorder type 3B Adrenoleukodystrophy, Neonatal cataract diabetes mellitus adult Refsum disease cholestasis hydrops fetalis intellectual disability arthrogryposis inborn errors of metabolism peroxisome biogenesis disorder 1A (Zellweger)

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, C	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.