4UQV | pdb_00004uqv

methanococcus jannaschii serine hydroxymethyl-transferase in complex with PLP

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)
L	d4uqvl_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
K	d4uqvk_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
J	d4uqvj_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
I	d4uqvi_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
H	d4uqvh_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
G	d4uqvg_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
F	d4uqvf_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
E	d4uqve_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D	d4uqvd_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d4uqvc_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d4uqvb_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
A	d4uqva_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	automated matches	automated matches	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2B (2022-06-29)
D	SCOP2 Family	GABA-aminotransferase-like	8075111	4000675	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PLP-dependent transferases	8075112	3000954	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)
L	Ribosomal_S8e	e4uqvL1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.2)
K	SIR2	e4uqvK1	A: beta barrels	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SIR2	ECOD (v294.2)
K	Phosphodiest, Metalloenzyme	e4uqvK2	A: beta barrels	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.2)
J	Ribosomal_S8e	e4uqvJ1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.2)
I	SIR2	e4uqvI3	A: beta barrels	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SIR2	ECOD (v294.2)
I	Phosphodiest, Metalloenzyme	e4uqvI2	A: beta barrels	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.2)
H	Ribosomal_S8e	e4uqvH1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.2)
G	Ribosomal_S8e	e4uqvG1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.2)
F	Ribosomal_S8e	e4uqvF1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.2)
E	SIR2	e4uqvE1	A: beta barrels	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SIR2	ECOD (v294.2)
E	Phosphodiest, Metalloenzyme	e4uqvE2	A: beta barrels	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Phosphodiest, Metalloenzyme	ECOD (v294.2)
D	Ribosomal_S8e	e4uqvD1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.2)
C	Penicil_amidase	e4uqvC1	A: beta barrels	X: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	H: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	T: Sulfite reductase hemoprotein (SiRHP), domains 2 and 4	F: Penicil_amidase	ECOD (v294.2)
B	Ribosomal_S8e	e4uqvB1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.2)
A	Ribosomal_S8e	e4uqvA1	A: beta barrels	X: Immunoglobulin-like beta-sandwich	H: Ribosomal protein L14-related	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
L	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
K	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
K	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
J	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
J	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
I	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
I	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
H	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
H	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
G	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
G	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
F	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
F	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
E	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
E	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
D	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
D	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)
C	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)
B	3.40.640.10	Alpha Beta	3-Layer(aba) Sandwich	Aspartate Aminotransferase	domain 2	CATH (4.3.0)
B	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)
A	3.90.1150.10	Alpha Beta	Alpha-Beta Complex	Aspartate Aminotransferase, domain 1	Aspartate Aminotransferase, domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	PF00464	Serine hydroxymethyltransferase (SHMT)	Serine hydroxymethyltransferase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	SERINE HYDROXYMETHYLTRANSFERASE	threonine aldolase activity L-allo-threonine aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding threonine aldolase activity L-allo-threonine aldolase activity lyase activity catalytic activity carbon-carbon lyase activity aldehyde-lyase activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding anion binding heterocyclic compound binding small molecule binding transferase activity, transferring one-carbon groups glycine hydroxymethyltransferase activity transferase activity hydroxymethyl-, formyl- and related transferase activity	folic acid-containing compound metabolic process modified amino acid metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process tetrahydrofolate interconversion small molecule metabolic process one-carbon metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR039429	Serine hydroxymethyltransferase-like domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR001085	Serine hydroxymethyltransferase	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR049943	Serine hydroxymethyltransferase-like	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	IPR019798	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	Binding Site

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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.