1W2W

Crystal structure of yeast Ypr118w, a methylthioribose-1-phosphate isomerase related to regulatory eIF2B subunits

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
A	d1w2w.1	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative methylthioribose-1-phosphate isomerase Ypr118W	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C [auth E]	d1w2w.2	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative methylthioribose-1-phosphate isomerase Ypr118W	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E [auth I]	d1w2w.3	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative methylthioribose-1-phosphate isomerase Ypr118W	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
G [auth M]	d1w2w.4	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative methylthioribose-1-phosphate isomerase Ypr118W	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D [auth F]	d1w2w.2	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative methylthioribose-1-phosphate isomerase Ypr118W	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
H [auth N]	d1w2w.4	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative methylthioribose-1-phosphate isomerase Ypr118W	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1w2w.1	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative methylthioribose-1-phosphate isomerase Ypr118W	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F [auth J]	d1w2w.3	Alpha and beta proteins (a/b)	NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	IF2B-like	Putative methylthioribose-1-phosphate isomerase Ypr118W	BAKER'S YEAST (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	IF-2B_N	e1w2wA1	A: alpha bundles	X: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	H: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	T: Translation initiation factor eIF-2B delta subunit N-terminal helical domain	F: IF-2B_N	ECOD (1.6)
C [auth E]	IF-2B_N	e1w2wE1	A: alpha bundles	X: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	H: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	T: Translation initiation factor eIF-2B delta subunit N-terminal helical domain	F: IF-2B_N	ECOD (1.6)
E [auth I]	IF-2B_N	e1w2wI1	A: alpha bundles	X: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	H: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	T: Translation initiation factor eIF-2B delta subunit N-terminal helical domain	F: IF-2B_N	ECOD (1.6)
G [auth M]	IF-2B_N	e1w2wM1	A: alpha bundles	X: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	H: Translation initiation factor eIF-2B delta subunit N-terminal helical domain (From Topology)	T: Translation initiation factor eIF-2B delta subunit N-terminal helical domain	F: IF-2B_N	ECOD (1.6)
D [auth F]	IF-2B_C	e1w2wF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: IF-2B_C	ECOD (1.6)
H [auth N]	IF-2B_C	e1w2wN1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: IF-2B_C	ECOD (1.6)
F [auth J]	IF-2B_C	e1w2wJ1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NagB/RpiA/CoA transferase-like	F: IF-2B_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.420	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	translation initiation factor eif-2b, domain 1	CATH (4.3.0)
C [auth E]	1.20.120.420	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	translation initiation factor eif-2b, domain 1	CATH (4.3.0)
E [auth I]	1.20.120.420	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	translation initiation factor eif-2b, domain 1	CATH (4.3.0)
G [auth M]	1.20.120.420	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	translation initiation factor eif-2b, domain 1	CATH (4.3.0)
D [auth F]	3.40.50.10470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor eif-2b	CATH (4.3.0)
H [auth N]	3.40.50.10470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor eif-2b	CATH (4.3.0)
B	3.40.50.10470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor eif-2b	CATH (4.3.0)
F [auth J]	3.40.50.10470	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Translation initiation factor eif-2b	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth E], E [auth I], G [auth M]	PF01008	Initiation factor 2 subunit family (IF-2B)	Initiation factor 2 subunit family	-	Family
B, D [auth F], F [auth J], H [auth N]	PF01008	Initiation factor 2 subunit family (IF-2B)	Initiation factor 2 subunit family	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth E], E [auth I], G [auth M]	5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE	isomerase activity S-methyl-5-thioribose-1-phosphate isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity catalytic activity	oxoacid metabolic process cellular biosynthetic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process oxoacid metabolic process cellular biosynthetic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process cellular metabolic compound salvage methionine biosynthetic process organonitrogen compound metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process methionine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid salvage amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process L-methionine salvage from methylthioadenosine proteinogenic amino acid biosynthetic process metabolic process cellular process L-methionine salvage sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process S-adenosylmethionine metabolic process S-adenosylmethionine cycle L-methionine salvage from S-adenosylmethionine	intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
B, D [auth F], F [auth J], H [auth N]	5-METHYLTHIORIBOSE-1-PHOSPHATE ISOMERASE	isomerase activity S-methyl-5-thioribose-1-phosphate isomerase activity intramolecular oxidoreductase activity, interconverting aldoses and ketoses intramolecular oxidoreductase activity catalytic activity	oxoacid metabolic process cellular biosynthetic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process oxoacid metabolic process cellular biosynthetic process sulfur amino acid metabolic process aspartate family amino acid biosynthetic process organonitrogen compound biosynthetic process aspartate family amino acid metabolic process amino acid metabolic process organic acid biosynthetic process organic acid metabolic process alpha-amino acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process organic substance biosynthetic process small molecule metabolic process sulfur compound metabolic process L-methionine biosynthetic process cellular metabolic compound salvage methionine biosynthetic process organonitrogen compound metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process L-amino acid biosynthetic process primary metabolic process methionine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid salvage amino acid biosynthetic process sulfur compound biosynthetic process biosynthetic process L-methionine salvage from methylthioadenosine proteinogenic amino acid biosynthetic process metabolic process cellular process L-methionine salvage sulfur amino acid biosynthetic process alpha-amino acid biosynthetic process S-adenosylmethionine metabolic process S-adenosylmethionine cycle L-methionine salvage from S-adenosylmethionine	intracellular anatomical structure cytoplasm cellular anatomical entity membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth E], E [auth I], G [auth M]	IPR042529	Initiation factor 2B-like, C-terminal	Homologous Superfamily
A, C [auth E], E [auth I], G [auth M]	IPR037171	NagB/RpiA transferase-like	Homologous Superfamily
A, C [auth E], E [auth I], G [auth M]	IPR000649	Initiation factor 2B-related	Family
A, C [auth E], E [auth I], G [auth M]	IPR011559	Initiation factor 2B alpha/beta/delta	Family
A, C [auth E], E [auth I], G [auth M]	IPR027363	Methylthioribose-1-phosphate isomerase, N-terminal	Homologous Superfamily
A, C [auth E], E [auth I], G [auth M]	IPR005251	Methylthioribose-1-phosphate isomerase	Family
B, D [auth F], F [auth J], H [auth N]	IPR042529	Initiation factor 2B-like, C-terminal	Homologous Superfamily
B, D [auth F], F [auth J], H [auth N]	IPR037171	NagB/RpiA transferase-like	Homologous Superfamily
B, D [auth F], F [auth J], H [auth N]	IPR000649	Initiation factor 2B-related	Family
B, D [auth F], F [auth J], H [auth N]	IPR011559	Initiation factor 2B alpha/beta/delta	Family
B, D [auth F], F [auth J], H [auth N]	IPR027363	Methylthioribose-1-phosphate isomerase, N-terminal	Homologous Superfamily
B, D [auth F], F [auth J], H [auth N]	IPR005251	Methylthioribose-1-phosphate isomerase	Family

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.