1YP3 | pdb_00001yp3

Crystal structure of potato tuber ADP-glucose pyrophosphorylase in complex with ATP

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d1yp3d1	All beta proteins	Single-stranded left-handed beta-helix	Trimeric LpxA-like enzymes	GlmU C-terminal domain-like	Glucose-1-phosphate adenylyltransferase small subunit, C-terminal domain	potato (Solanum tuberosum ) [TaxId: 4113 ],	SCOPe (2.08)
D	d1yp3d2	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	glucose-1-phosphate thymidylyltransferase	Glucose-1-phosphate adenylyltransferase small subunit, catalytic domain	potato (Solanum tuberosum ) [TaxId: 4113 ],	SCOPe (2.08)
C	d1yp3c1	All beta proteins	Single-stranded left-handed beta-helix	Trimeric LpxA-like enzymes	GlmU C-terminal domain-like	Glucose-1-phosphate adenylyltransferase small subunit, C-terminal domain	potato (Solanum tuberosum ) [TaxId: 4113 ],	SCOPe (2.08)
C	d1yp3c2	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	glucose-1-phosphate thymidylyltransferase	Glucose-1-phosphate adenylyltransferase small subunit, catalytic domain	potato (Solanum tuberosum ) [TaxId: 4113 ],	SCOPe (2.08)
B	d1yp3b1	All beta proteins	Single-stranded left-handed beta-helix	Trimeric LpxA-like enzymes	GlmU C-terminal domain-like	Glucose-1-phosphate adenylyltransferase small subunit, C-terminal domain	potato (Solanum tuberosum ) [TaxId: 4113 ],	SCOPe (2.08)
B	d1yp3b2	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	glucose-1-phosphate thymidylyltransferase	Glucose-1-phosphate adenylyltransferase small subunit, catalytic domain	potato (Solanum tuberosum ) [TaxId: 4113 ],	SCOPe (2.08)
A	d1yp3a1	All beta proteins	Single-stranded left-handed beta-helix	Trimeric LpxA-like enzymes	GlmU C-terminal domain-like	Glucose-1-phosphate adenylyltransferase small subunit, C-terminal domain	potato (Solanum tuberosum ) [TaxId: 4113 ],	SCOPe (2.08)
A	d1yp3a2	Alpha and beta proteins (a/b)	Nucleotide-diphospho-sugar transferases	Nucleotide-diphospho-sugar transferases	glucose-1-phosphate thymidylyltransferase	Glucose-1-phosphate adenylyltransferase small subunit, catalytic domain	potato (Solanum tuberosum ) [TaxId: 4113 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8034826	3001804	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8034827	3000077	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8034827	3000077	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8034826	3001804	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8034826	3001804	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8034827	3000077	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Trimeric LpxA-like enzymes	8034826	3001804	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8034827	3000077	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)
D		e1yp3D1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
D		e1yp3D2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)
C		e1yp3C1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
C		e1yp3C2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)
B		e1yp3B1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
B		e1yp3B2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)
A		e1yp3A1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: Peptidase_C1	F:	ECOD (20:10:01)
A		e1yp3A2	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: E1_dh	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
D	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
C	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
C	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
B	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
B	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)
A	3.90.550.10	Alpha Beta	Alpha-Beta Complex	Spore Coat Polysaccharide Biosynthesis Protein SpsA	Chain A	CATH (4.3.0)
A	2.160.10.10	Mainly Beta	3 Solenoid	UDP N-Acetylglucosamine Acyltransferase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF25247	GLGC left-handed parallel beta-helix domain (LbH_GLGC)	GLGC left-handed parallel beta-helix domain	-	Repeat
A, B, C, D	PF00483	Nucleotidyl transferase (NTP_transferase)	Nucleotidyl transferase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Glucose-1-phosphate adenylyltransferase small subunit	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 adenylyltransferase activity glucose-1-phosphate adenylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	carbohydrate metabolic process glucan biosynthetic process polysaccharide biosynthetic process carbohydrate biosynthetic process primary metabolic process macromolecule biosynthetic process polysaccharide metabolic process glucan metabolic process biosynthetic process starch metabolic process metabolic process cellular process macromolecule metabolic process starch biosynthetic process carbohydrate metabolic process glucan biosynthetic process polysaccharide biosynthetic process carbohydrate biosynthetic process primary metabolic process macromolecule biosynthetic process polysaccharide metabolic process glucan metabolic process biosynthetic process starch metabolic process metabolic process cellular process macromolecule metabolic process starch biosynthetic process energy derivation by oxidation of organic compounds glycogen metabolic process generation of precursor metabolites and energy glycogen biosynthetic process energy reserve metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle amyloplast chloroplast transferase complex, transferring phosphorus-containing groups protein-containing complex glucose-1-phosphate adenylyltransferase complex catalytic complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure plastid organelle cytoplasm intracellular membrane-bounded organelle amyloplast chloroplast transferase complex, transferring phosphorus-containing groups protein-containing complex glucose-1-phosphate adenylyltransferase complex catalytic complex adenylyltransferase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR011831	Glucose-1-phosphate adenylyltransferase	Family
A, B, C, D	IPR005836	ADP-glucose pyrophosphorylase, conserved site	Conserved Site
A, B, C, D	IPR011004	Trimeric LpxA-like superfamily	Homologous Superfamily
A, B, C, D	IPR005835	Nucleotidyl transferase domain	Domain
A, B, C, D	IPR029044	Nucleotide-diphospho-sugar transferases	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.