5YJL | pdb_00005yjl

Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with NADPH and GBP

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Glutamyl tRNA-reductase dimerization domain	8091375	3000027	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8091366	3001023	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glutamyl tRNA-reductase coenzyme-binding domain-like	8089294	3000056	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Glutamyl tRNA-reductase coenzyme-binding domain-like	8089294	3000056	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Glutamyl tRNA-reductase dimerization domain	8091375	3000027	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8091366	3001023	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	Yippee-Mis18	e5yjlA1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Yippee-Mis18	ECOD (v294.1)
C [auth B]	DEAD	e5yjlB1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (v294.1)
B [auth C]	DEAD	e5yjlC1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (v294.1)
D	Yippee-Mis18	e5yjlD1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Yippee-Mis18	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.460.30	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C [auth B]	3.30.460.30	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
C [auth B]	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B [auth C]	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
B [auth C]	3.20.180.10	Alpha Beta	Alpha-Beta Barrel	Split barrel-like	PNP-oxidase-like	CATH (4.3.0)
D	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
D	3.20.180.10	Alpha Beta	Alpha-Beta Barrel	Split barrel-like	PNP-oxidase-like	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF00745	Glutamyl-tRNAGlu reductase, dimerisation domain (GlutR_dimer)	Glutamyl-tRNAGlu reductase, dimerisation domain		Domain
A, C [auth B]	PF05201	Glutamyl-tRNAGlu reductase, N-terminal domain (GlutR_N)	Glutamyl-tRNAGlu reductase, N-terminal domain		Domain
A, C [auth B]	PF01488	Shikimate / quinate 5-dehydrogenase (Shikimate_DH)	Shikimate / quinate 5-dehydrogenase	-	Family
B [auth C], D	PF10615	Domain of unknown function (DUF2470) (DUF2470)	Domain of unknown function (DUF2470)	This domain is found in a group of putative heme-iron utilisation proteins, such as HugZ. It can also be found in C-terminal of the glutamyl-tRNA reductase-binding (GluTRBP) protein from Arabidopsis [1]. GluTRBP is involved in the regulation of gluta ...	This domain is found in a group of putative heme-iron utilisation proteins, such as HugZ. It can also be found in C-terminal of the glutamyl-tRNA reductase-binding (GluTRBP) protein from Arabidopsis [1]. GluTRBP is involved in the regulation of glutamyl-tRNA reductase (GluTR) which is important for the synthesis and distribution of 5-aminolevulinate, a precursor in heme and chlorophyll biosynthesis [2]. GluTRBP is necessary for efficient photosynthetic electron transport in chloroplasts [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	Glutamyl-tRNA reductase 1	binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity catalytic activity, acting on RNA oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity, acting on a nucleic acid glutamyl-tRNA reductase activity catalytic activity, acting on a tRNA binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding oxidoreductase activity catalytic activity, acting on RNA oxidoreductase activity, acting on the aldehyde or oxo group of donors catalytic activity, acting on a nucleic acid glutamyl-tRNA reductase activity catalytic activity, acting on a tRNA catalytic activity oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process chlorophyll biosynthetic process heme metabolic process heme biosynthetic process protoporphyrinogen IX metabolic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process chlorophyll biosynthetic process heme metabolic process heme biosynthetic process protoporphyrinogen IX metabolic process protoporphyrinogen IX biosynthetic process response to light stimulus response to stimulus response to radiation response to abiotic stimulus	membrane-bounded organelle plastid membrane intracellular anatomical structure plastid membrane chloroplast envelope intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure chloroplast membrane organelle cytoplasm organelle membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid membrane chloroplast envelope intracellular membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure chloroplast membrane organelle cytoplasm organelle membrane plastid envelope chloroplast protein-containing complex
B [auth C], D	Glutamyl-tRNA reductase-binding protein	protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process chlorophyll biosynthetic process heme metabolic process regulation of cellular process heme biosynthetic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole metabolic process chlorophyll metabolic process pigment biosynthetic process tetrapyrrole biosynthetic process biosynthetic process metabolic process cellular process porphyrin-containing compound metabolic process chlorophyll biosynthetic process heme metabolic process regulation of cellular process heme biosynthetic process positive regulation of biological process positive regulation of tetrapyrrole biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of tetrapyrrole biosynthetic process positive regulation of heme biosynthetic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of heme biosynthetic process biological regulation regulation of tetrapyrrole metabolic process regulation of metabolic process photosynthesis photosynthesis, light reaction photosynthetic electron transport chain electron transport chain generation of precursor metabolites and energy developmental process multicellular organism development multicellular organismal process anatomical structure development post-embryonic development	membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast intracellular membraneless organelle plastid thylakoid chloroplast thylakoid membrane-bounded organelle intracellular anatomical structure plastid intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure plastid stroma organelle chloroplast stroma cytoplasm chloroplast intracellular membraneless organelle plastid thylakoid chloroplast thylakoid membraneless organelle thylakoid protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR018214	Glutamyl-tRNA reductase, conserved site	Conserved Site
A, C [auth B]	IPR006151	Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase	Domain
A, C [auth B]	IPR015895	Glutamyl-tRNA reductase, N-terminal	Domain
A, C [auth B]	IPR000343	Glutamyl-tRNA reductase	Family
A, C [auth B]	IPR036453	Glutamyl tRNA-reductase dimerization domain superfamily	Homologous Superfamily
A, C [auth B]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, C [auth B]	IPR036343	Glutamyl-tRNA reductase, N-terminal domain superfamily	Homologous Superfamily
A, C [auth B]	IPR015896	Tetrapyrrole biosynthesis, glutamyl-tRNA reductase, dimerisation domain	Domain
B [auth C], D	IPR012349	FMN-binding split barrel	Homologous Superfamily
B [auth C], D	IPR019595	Domain of unknown function DUF2470	Domain
B [auth C], D	IPR037119	Haem oxygenase HugZ-like 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.