3WDM | pdb_00003wdm

Crystal structure of 4-phosphopantoate-beta-alanine ligase from Thermococcus kodakarensis

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	CBM_4_9	e3wdmB1	A: a/b three-layered sandwiches	X: jelly-roll	H: Galactose-binding domain-like	T: Galactose-binding domain-like	F: CBM_4_9	ECOD (v294.1)
C	CBM_4_9	e3wdmC1	A: a/b three-layered sandwiches	X: jelly-roll	H: Galactose-binding domain-like	T: Galactose-binding domain-like	F: CBM_4_9	ECOD (v294.1)
D	CBM_4_9	e3wdmD1	A: a/b three-layered sandwiches	X: jelly-roll	H: Galactose-binding domain-like	T: Galactose-binding domain-like	F: CBM_4_9	ECOD (v294.1)
A	RVP	e3wdmA1	A: a/b three-layered sandwiches	X: DEATH domain	H: HTH	T: winged helix domain	F: RVP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.12640	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphopantoate/pantothenate synthetase	CATH (4.3.0)
C	3.40.50.12640	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphopantoate/pantothenate synthetase	CATH (4.3.0)
D	3.40.50.12640	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphopantoate/pantothenate synthetase	CATH (4.3.0)
A	3.40.50.12640	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Phosphopantoate/pantothenate synthetase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02006	Phosphopantothenate/pantothenate synthetase (PPS_PS)	Phosphopantothenate/pantothenate synthetase	This family of archaeal proteins includes pantothenate synthetase from Methanosarcina mazei and 4-phosphopantoate--beta-alanine ligase (phosphopantothenate synthetase) from Pyrococcus kodakaraensis. Pantothenate synthetase catalyses the condensation ...	This family of archaeal proteins includes pantothenate synthetase from Methanosarcina mazei and 4-phosphopantoate--beta-alanine ligase (phosphopantothenate synthetase) from Pyrococcus kodakaraensis. Pantothenate synthetase catalyses the condensation of pantoate with beta-alanine in an ATP-dependent and ADP-producing reaction [1]. 4-phosphopantoate--beta-alanine ligase catalyses the conversion of (R)-4-phosphopantoate and beta-alanine to 4'-phosphopantothenate in the CoA biosynthesis pathway. It cannot use (R)-pantoate as substrate and thus does not display pantothenate synthetase activity [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	4-phosphopantoate--beta-alanine ligase	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding acid-amino acid ligase activity catalytic activity ligase activity, forming carbon-nitrogen bonds ligase activity	nucleoside phosphate metabolic process coenzyme A biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process nucleoside phosphate metabolic process coenzyme A biosynthetic process primary metabolic process nucleobase-containing compound biosynthetic process purine-containing compound metabolic process nucleobase-containing compound metabolic process sulfur compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleobase-containing small molecule metabolic process purine-containing compound biosynthetic process nucleoside phosphate biosynthetic process phosphate-containing compound metabolic process metabolic process cellular process small molecule metabolic process sulfur compound metabolic process phosphorus metabolic process coenzyme A metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002855	Phosphopantoate/pantothenate synthetase	Family
A, B, C, D	IPR038138	Phosphopantoate/pantothenate synthetase superfamily	Homologous Superfamily

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.