5DQR

The crystal structure of Arabidopsis 7-hydroxymethyl chlorophyll a reductase (HCAR)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	FrhB/FdhB-like	8045890	4004744	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FrhB/FdhB-like	8045906	3002602	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	FrhB/FdhB-like	8045906	3002602	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FrhB/FdhB-like	8045906	3002602	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	FrhB/FdhB-like	8045906	3002602	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	FrhB/FdhB-like	8045906	3002602	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	FrhB/FdhB-like	8045906	3002602	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	PF04422,PF04432	e5dqrA1	A: alpha arrays	X: F420-reducing hydrogenase subunit beta (From Topology)	H: F420-reducing hydrogenase subunit beta (From Topology)	T: F420-reducing hydrogenase subunit beta	F: PF04422,PF04432	ECOD (1.6)
B	PF04422,PF04432	e5dqrB1	A: alpha arrays	X: F420-reducing hydrogenase subunit beta (From Topology)	H: F420-reducing hydrogenase subunit beta (From Topology)	T: F420-reducing hydrogenase subunit beta	F: PF04422,PF04432	ECOD (1.6)
C	PF04422,PF04432	e5dqrC1	A: alpha arrays	X: F420-reducing hydrogenase subunit beta (From Topology)	H: F420-reducing hydrogenase subunit beta (From Topology)	T: F420-reducing hydrogenase subunit beta	F: PF04422,PF04432	ECOD (1.6)
D	PF04422,PF04432	e5dqrD1	A: alpha arrays	X: F420-reducing hydrogenase subunit beta (From Topology)	H: F420-reducing hydrogenase subunit beta (From Topology)	T: F420-reducing hydrogenase subunit beta	F: PF04422,PF04432	ECOD (1.6)
E	PF04422,PF04432	e5dqrE1	A: alpha arrays	X: F420-reducing hydrogenase subunit beta (From Topology)	H: F420-reducing hydrogenase subunit beta (From Topology)	T: F420-reducing hydrogenase subunit beta	F: PF04422,PF04432	ECOD (1.6)
F	PF04422,PF04432	e5dqrF1	A: alpha arrays	X: F420-reducing hydrogenase subunit beta (From Topology)	H: F420-reducing hydrogenase subunit beta (From Topology)	T: F420-reducing hydrogenase subunit beta	F: PF04422,PF04432	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF04422	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term (FrhB_FdhB_N)	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit N-term	-	Family
A, B, C, D, E A, B, C, D, E, F	PF04432	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus (FrhB_FdhB_C)	Coenzyme F420 hydrogenase/dehydrogenase, beta subunit C terminus	Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum fo ...	Coenzyme F420 hydrogenase (EC:1.12.99.1) reduces the low-potential two-electron acceptor coenzyme F420. This family contains the C termini of F420 hydrogenase and dehydrogenase beta subunits [1], [2]. The N terminus of Methanobacterium formicicum formate dehydrogenase beta chain (EC:1.2.1.2, Swiss:P06130) is also a member of this family [3]. This region is often found in association with the 4Fe-4S binding domain, fer4 (Pfam:PF00037).	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	7-hydroxymethyl chlorophyll a reductase, chloroplastic	iron-sulfur cluster binding binding metal cluster binding small molecule binding oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups 7-hydroxymethyl chlorophyll a reductase activity catalytic activity cation binding ion binding metal ion binding	organic cyclic compound metabolic process organic substance metabolic process organonitrogen compound metabolic process tetrapyrrole metabolic process chlorophyll metabolic process metabolic process porphyrin-containing compound metabolic process chlorophyll cycle	membrane-bounded organelle intracellular organelle intracellular anatomical structure plastid organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle chloroplast extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR045220	Oxidoreductase FRHB/FDHB/HCAR-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR007516	Coenzyme F420 hydrogenase/dehydrogenase beta subunit, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR007525	Coenzyme F420 hydrogenase/dehydrogenase beta subunit, C-terminal	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
D	7-hydroxymethyl chlorophyll A reductase (HCAR) M-CSA #990	7-Hydroxymethyl chlorophyll (HCAR) is a member of the family of chlorophyll catabolic enzymes (CCEs). Its a reductase that catalyses one of the reactions in chlorophyll conversion. HCAR is required for the degradation of light-harvesting complexes and is necessary for efficient photosynthesis by balancing the chlorophyll A/B ratio. Specifically, its a protein containing both 4Fe-4S complexes and FAD cofactor that converts 7-hydroxymethyl chlorophyll (HMChl) a to chlorophyll A using ferredoxin for reduction of the substrate. HCAR catalyses the reduction of a hydroxymethyl group to a methyl group.	Defined by 4 residues: ASP:D-212 [auth D-237]GLU:D-237 [auth D-262]GLN:D-307 [auth D-332]HIS:D-392 [auth D-417] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.17.7.2 (PDB Primary Data) Search M-CSA Motif + EC 1.17.7.2

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 R01GM133198.