2ZR8

Crystal Structure of Modified Serine Racemase complexed with Serine

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	d2zr8a_	Alpha and beta proteins (a/b)	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	Tryptophan synthase beta subunit-like PLP-dependent enzymes	automated matches	Fission yeast (Schizosaccharomyces pombe ) [TaxId: 4896 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Tryptophan synthase beta subunit-like PLP-dependent enzymes	8033042	3001427	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	PF00291	e2zr8A2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Tryptophan synthase beta subunit-like PLP-dependent enzymes (From Topology)	T: Tryptophan synthase beta subunit-like PLP-dependent enzymes	F: PF00291	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.1100	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00291	Pyridoxal-phosphate dependent enzyme (PALP)	Pyridoxal-phosphate dependent enzyme	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Uncharacterized protein C320.14	L-serine ammonia-lyase activity lyase activity ammonia-lyase activity catalytic activity carbon-nitrogen lyase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding L-serine ammonia-lyase activity lyase activity ammonia-lyase activity catalytic activity carbon-nitrogen lyase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding racemase activity, acting on amino acids and derivatives isomerase activity racemase and epimerase activity racemase and epimerase activity, acting on amino acids and derivatives amino-acid racemase activity threonine racemase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity vitamin binding vitamin B6 binding pyridoxal phosphate binding serine racemase activity D-serine ammonia-lyase activity	organonitrogen compound metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process D-serine metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process organic substance metabolic process D-amino acid metabolic process metabolic process small molecule metabolic process organonitrogen compound metabolic process oxoacid metabolic process cellular metabolic process carboxylic acid metabolic process amino acid metabolic process primary metabolic process organic acid metabolic process D-serine metabolic process alpha-amino acid metabolic process non-proteinogenic amino acid metabolic process organic substance metabolic process D-amino acid metabolic process metabolic process small molecule metabolic process cellular process serine family amino acid metabolic process L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036052	Tryptophan synthase beta chain-like, PALP domain superfamily	Homologous Superfamily
A	IPR001926	Tryptophan synthase beta chain-like, PALP domain	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	serine racemase M-CSA #330	Serine racemase (SRR) catalyses the PLP-dependent synthesis of D-serine from L-serine (and vice versa. SRR also has dehydratase activity towards both L-serine and D-serine, resulting in pyruvate and ammonia. It is allosterically activated by ATP, by magnesium, and possibly also by other divalent metal cations. The magnesium ion present in the crystal structure is thought to be essential for the structural integrity of the enzymes, and not directly involved in catalysis [PMID:20564571].	Defined by 6 residues: LYS:A-57SER:A-82GLU:A-208GLY:A-212ASP:A-214SER:A-308 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 5.1.1.18 (PDB Primary Data) Search M-CSA Motif + EC 5.1.1.18
A	L-serine ammonia-lyase M-CSA #956	serine racemase (SRR) catalyses the PLP-dependent synthesis of D-serine from L-serine (and vice versa. SRR also has dehydratase activity towards both L-serine and D-serine, resulting in pyruvate and ammonia. It is allosterically activated by ATP, by magnesium, and possibly also by other divalent metal cations. The magnesium ion present in the crystal structure is thought to be essential for the structural integrity of the enzymes, and not directly involved in catalysis [PMID:20564571].	Defined by 6 residues: LYS:A-57SER:A-82GLU:A-208GLY:A-212ASP:A-214SER:A-308 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 5.1.1.18 (PDB Primary Data) Search M-CSA Motif + EC 5.1.1.18

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 R01GM133198.