5CHE

Crystal structure of Arabidopsis glutamyl-tRNA reductase in complex with its regulatory proteins

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 coenzyme-binding domain-like	8089294	3000056	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 dimerization domain	8091375	3000027	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutamyl tRNA-reductase coenzyme-binding domain-like	8089294	3000056	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Eukaryotic type KH-domain (KH-domain type I)	8091366	3001023	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glutamyl tRNA-reductase dimerization domain	8091375	3000027	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	GlutR_dimer	e5cheA1	A: alpha duplicates or obligate multimers	X: Glutamyl tRNA-reductase dimerization domain (From Topology)	H: Glutamyl tRNA-reductase dimerization domain (From Topology)	T: Glutamyl tRNA-reductase dimerization domain	F: GlutR_dimer	ECOD (1.6)
A	GlutR_N	e5cheA3	A: a+b two layers	X: Alpha-beta plaits	H: Glutamyl tRNA-reductase catalytic, N-terminal domain (From Topology)	T: Glutamyl tRNA-reductase catalytic, N-terminal domain	F: GlutR_N	ECOD (1.6)
A	OCD_Mu_crystall_C	e5cheA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: OCD_Mu_crystall_C	ECOD (1.6)
B	GlutR_dimer	e5cheB1	A: alpha duplicates or obligate multimers	X: Glutamyl tRNA-reductase dimerization domain (From Topology)	H: Glutamyl tRNA-reductase dimerization domain (From Topology)	T: Glutamyl tRNA-reductase dimerization domain	F: GlutR_dimer	ECOD (1.6)
B	GlutR_N	e5cheB3	A: a+b two layers	X: Alpha-beta plaits	H: Glutamyl tRNA-reductase catalytic, N-terminal domain (From Topology)	T: Glutamyl tRNA-reductase catalytic, N-terminal domain	F: GlutR_N	ECOD (1.6)
B	OCD_Mu_crystall_C	e5cheB2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: OCD_Mu_crystall_C	ECOD (1.6)
C	Pyrid_oxidase_2	e5cheC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Pyrid_oxidase_2	ECOD (1.6)
C	DUF2470	e5cheC2	A: a+b two layers	X: a+b domain in heme oxygenase (From Topology)	H: a+b domain in heme oxygenase (From Topology)	T: a+b domain in heme oxygenase	F: DUF2470	ECOD (1.6)
D	Pyrid_oxidase_2	e5cheD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Pyrid_oxidase_2	ECOD (1.6)
D	DUF2470	e5cheD2	A: a+b two layers	X: a+b domain in heme oxygenase (From Topology)	H: a+b domain in heme oxygenase (From Topology)	T: a+b domain in heme oxygenase	F: DUF2470	ECOD (1.6)
E	TPR_11_1	e5cheE1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TPR_11_1	ECOD (1.6)
F	TPR_11_1	e5cheF1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TPR_11_1	ECOD (1.6)

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)
B	3.30.460.30	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
C	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
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)
E	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)
F	1.25.40.10	Mainly Alpha	Alpha Horseshoe	Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat	Tetratricopeptide repeat domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00745	Glutamyl-tRNAGlu reductase, dimerisation domain (GlutR_dimer)	Glutamyl-tRNAGlu reductase, dimerisation domain	-	Domain
A, B	PF05201	Glutamyl-tRNAGlu reductase, N-terminal domain (GlutR_N)	Glutamyl-tRNAGlu reductase, N-terminal domain	-	Domain
A, B	PF01488	Shikimate / quinate 5-dehydrogenase (Shikimate_DH)	Shikimate / quinate 5-dehydrogenase	-	Family
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
E, F	PF13424	Tetratricopeptide repeat (TPR_12)	Tetratricopeptide repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Glutamyl-tRNA reductase 1, chloroplastic	binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound 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 binding nucleoside phosphate binding purine nucleotide binding organic cyclic compound 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 biosynthetic process tetrapyrrole metabolic process biosynthetic process chlorophyll metabolic process pigment biosynthetic process metabolic process porphyrin-containing compound metabolic process chlorophyll biosynthetic process heme metabolic process heme biosynthetic process protoporphyrinogen IX metabolic process protoporphyrinogen IX biosynthetic process	membrane-bounded organelle plastid membrane intracellular anatomical structure plastid membrane chloroplast envelope cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle organelle envelope chloroplast membrane organelle cytoplasm organelle membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid membrane chloroplast envelope cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle organelle envelope chloroplast membrane organelle cytoplasm organelle membrane plastid envelope chloroplast protein-containing complex
C, D	Glutamyl-tRNA reductase-binding protein, chloroplastic	protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity	pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole biosynthetic process tetrapyrrole metabolic process biosynthetic process chlorophyll metabolic process pigment biosynthetic process metabolic process porphyrin-containing compound metabolic process chlorophyll biosynthetic process heme metabolic process heme biosynthetic process positive regulation of biological process positive regulation of tetrapyrrole biosynthetic process pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole biosynthetic process tetrapyrrole metabolic process biosynthetic process chlorophyll metabolic process pigment biosynthetic process metabolic process porphyrin-containing compound metabolic process chlorophyll biosynthetic process heme metabolic 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 regulation of biosynthetic process regulation of biological process regulation of heme biosynthetic process biological regulation positive regulation of tetrapyrrole metabolic process regulation of tetrapyrrole metabolic process regulation of metabolic process photosynthesis photosynthesis, light reaction photosynthetic electron transport chain cellular metabolic process electron transport chain cellular process 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 cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle plastid stroma organelle chloroplast stroma cytoplasm chloroplast plastid thylakoid chloroplast thylakoid intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure plastid cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle plastid stroma organelle chloroplast stroma cytoplasm chloroplast plastid thylakoid chloroplast thylakoid intracellular non-membrane-bounded organelle thylakoid non-membrane-bounded organelle protein-containing complex
E, F	Protein FLUORESCENT IN BLUE LIGHT, chloroplastic	-	pigment metabolic process porphyrin-containing compound biosynthetic process tetrapyrrole biosynthetic process tetrapyrrole metabolic process biosynthetic process chlorophyll metabolic process pigment biosynthetic process metabolic process porphyrin-containing compound metabolic process chlorophyll biosynthetic process	chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope bounding membrane of organelle thylakoid plastid envelope chloroplast chloroplast thylakoid membrane membrane-bounded organelle plastid membrane intracellular anatomical structure plastid organelle outer membrane plastid thylakoid membrane plastid thylakoid intracellular organelle organelle envelope bounding membrane of organelle thylakoid plastid envelope chloroplast non-membrane-bounded organelle membrane cellular anatomical entity intracellular membrane-bounded organelle thylakoid membrane organelle chloroplast thylakoid intracellular non-membrane-bounded organelle outer membrane cytoplasm photosynthetic membrane organelle membrane chloroplast envelope chloroplast membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018214	Glutamyl-tRNA reductase, conserved site	Conserved Site
A, B	IPR006151	Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase	Domain
A, B	IPR015895	Glutamyl-tRNA reductase, N-terminal	Domain
A, B	IPR000343	Glutamyl-tRNA reductase	Family
A, B	IPR036453	Glutamyl tRNA-reductase dimerization domain superfamily	Homologous Superfamily
A, B	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B	IPR036343	Glutamyl-tRNA reductase, N-terminal domain superfamily	Homologous Superfamily
A, B	IPR015896	Tetrapyrrole biosynthesis, glutamyl-tRNA reductase, dimerisation domain	Domain
C, D	IPR012349	FMN-binding split barrel	Homologous Superfamily
C, D	IPR019595	Domain of unknown function DUF2470	Domain
C, D	IPR037119	Haem oxygenase HugZ-like superfamily	Homologous Superfamily
E, F	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
E, F	IPR044243	Protein FLUORESCENT IN BLUE LIGHT	Family

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.