2Y8N | pdb_00002y8n

Crystal structure of glycyl radical enzyme

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PFL-like	e2y8nA1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (1.6)
A	PFL-like	e2y8nA2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PFL-like	ECOD (1.6)
C	PFL-like	e2y8nC1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: PFL-like	ECOD (1.6)
C	PFL-like	e2y8nC2	A: extended segments	X: Glycyl radical domain (From Topology)	H: Glycyl radical domain (From Topology)	T: Glycyl radical domain	F: PFL-like	ECOD (1.6)
B	pdi_dom_like	e2y8nB2	A: few secondary structure elements	X: HIPIP (high potential iron protein) (From Topology)	H: HIPIP (high potential iron protein) (From Topology)	T: HIPIP (high potential iron protein)	F: pdi_dom_like	ECOD (1.6)
B	EUF08672	e2y8nB1	A: few secondary structure elements	X: HIPIP (high potential iron protein) (From Topology)	H: HIPIP (high potential iron protein) (From Topology)	T: HIPIP (high potential iron protein)	F: EUF08672	ECOD (1.6)
D	pdi_dom_like	e2y8nD2	A: few secondary structure elements	X: HIPIP (high potential iron protein) (From Topology)	H: HIPIP (high potential iron protein) (From Topology)	T: HIPIP (high potential iron protein)	F: pdi_dom_like	ECOD (1.6)
D	EUF08672	e2y8nD1	A: few secondary structure elements	X: HIPIP (high potential iron protein) (From Topology)	H: HIPIP (high potential iron protein) (From Topology)	T: HIPIP (high potential iron protein)	F: EUF08672	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
C	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
B	2.20.70.100	Mainly Beta	Single Sheet	Ubiquitin Ligase Nedd4	Chain: W	CATH (4.3.0)
D	2.20.70.100	Mainly Beta	Single Sheet	Ubiquitin Ligase Nedd4	Chain: W	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF01228	Glycine radical (Gly_radical)	Glycine radical		Domain
B, D	PF18671	4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal (4HPAD_g_N)	4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal	4-Hydroxyphenylacetate decarboxylase (4-HPAD) is a heterotetramer consisting of catalytic beta-subunit harboring the putative glycyl/thiyl dyad and a distinct small gamma-subunit with two [4Fe-4S] clusters (EC:4.1.1.83). The gamma-subunit is proposed ...	4-Hydroxyphenylacetate decarboxylase (4-HPAD) is a heterotetramer consisting of catalytic beta-subunit harboring the putative glycyl/thiyl dyad and a distinct small gamma-subunit with two [4Fe-4S] clusters (EC:4.1.1.83). The gamma-subunit is proposed to be involved in the regulation of the oligomeric state and catalytic activity of the enzyme and it comprises two domains with some amino acid sequence identity that are structurally related by a pseudo-2-fold symmetry indicating a gene duplication origin. This entry represents the N-terminal domain which binds one [4Fe-4S] cluster through His3, Cys6, Cys19, and Cys36 [1].	Domain
B, D	PF18524	High potential iron-sulfur protein like (HPIP_like)	High potential iron-sulfur protein like	This is a C-terminal domain found in 4-hydroxyphenylacetate decarboxylase small subunit (EC:4.1.1.83), which catalyzes the last reaction in the fermentative production of p-cresol from tyrosine. The C-terminal domain [4F-4S] cluster bears structural ...	This is a C-terminal domain found in 4-hydroxyphenylacetate decarboxylase small subunit (EC:4.1.1.83), which catalyzes the last reaction in the fermentative production of p-cresol from tyrosine. The C-terminal domain [4F-4S] cluster bears structural similarity to high-potential iron-sulfur proteins (HiPIPs). HiPIPs have an N-terminal extension of 20-40 residues, so the structural similarity is limited to their Fe/S cluster-binding scaffold. Furthermore, despite of the weak amino acid sequence identity, the cluster binding motifs are remarkably similar to H/CX2CX12-13CX16-17C for the gamma-subunit and CX2CX13-19CX14-19C for HiPIPs [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	4-HYDROXYPHENYLACETATE DECARBOXYLASE LARGE SUBUNIT	4-hydroxyphenylacetate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
B, D	4-HYDROXYPHENYLACETATE DECARBOXYLASE SMALL SUBUNIT	4-hydroxyphenylacetate decarboxylase activity carboxy-lyase activity lyase activity catalytic activity carbon-carbon lyase activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR051215	Glycyl Radical Enzyme	Family
A, C	IPR004184	Pyruvate formate lyase domain	Domain
A, C	IPR001150	Glycine radical domain	Domain
B, D	IPR041125	4-hydroxyphenylacetate decarboxylase small gamma subunit, N-terminal	Domain
B, D	IPR053727	HPA decarboxylase small subunit superfamily	Homologous Superfamily
B, D	IPR040923	4-hydroxyphenylacetate decarboxylase small gamma subunit, C-terminal	Domain

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.