6JUY

Crystal Structure of ArgZ, apo structure, an Arginine Dihydrolase from the Ornithine-Ammonia Cycle in Cyanobacteria

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)
B	COG1915_1st	e6juyB2	A: beta barrels	X: MMP1218-like (From Topology)	H: MMP1218-like (From Topology)	T: MMP1218-like	F: COG1915_1st	ECOD (1.6)
B	Saccharop_dh_N	e6juyB3	A: a+b two layers	X: Alpha-beta plaits	H: MJ1480-like (From Topology)	T: MJ1480-like	F: Saccharop_dh_N	ECOD (1.6)
B	Amidinotransf	e6juyB4	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: Amidinotransf	ECOD (1.6)
B	COG1915_2nd	e6juyB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: COG1915_2nd	ECOD (1.6)
D	COG1915_1st	e6juyD2	A: beta barrels	X: MMP1218-like (From Topology)	H: MMP1218-like (From Topology)	T: MMP1218-like	F: COG1915_1st	ECOD (1.6)
D	Saccharop_dh_N	e6juyD4	A: a+b two layers	X: Alpha-beta plaits	H: MJ1480-like (From Topology)	T: MJ1480-like	F: Saccharop_dh_N	ECOD (1.6)
D	Amidinotransf	e6juyD3	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: Amidinotransf	ECOD (1.6)
D	COG1915_2nd	e6juyD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: COG1915_2nd	ECOD (1.6)
A	COG1915_1st	e6juyA2	A: beta barrels	X: MMP1218-like (From Topology)	H: MMP1218-like (From Topology)	T: MMP1218-like	F: COG1915_1st	ECOD (1.6)
A	Saccharop_dh_N	e6juyA4	A: a+b two layers	X: Alpha-beta plaits	H: MJ1480-like (From Topology)	T: MJ1480-like	F: Saccharop_dh_N	ECOD (1.6)
A	Amidinotransf	e6juyA3	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: Amidinotransf	ECOD (1.6)
A	COG1915_2nd	e6juyA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: COG1915_2nd	ECOD (1.6)
C	COG1915_1st	e6juyC2	A: beta barrels	X: MMP1218-like (From Topology)	H: MMP1218-like (From Topology)	T: MMP1218-like	F: COG1915_1st	ECOD (1.6)
C	Saccharop_dh_N	e6juyC4	A: a+b two layers	X: Alpha-beta plaits	H: MJ1480-like (From Topology)	T: MJ1480-like	F: Saccharop_dh_N	ECOD (1.6)
C	Amidinotransf	e6juyC3	A: a+b duplicates or obligate multimers	X: Pentein (From Topology)	H: Pentein (From Topology)	T: Pentein	F: Amidinotransf	ECOD (1.6)
C	COG1915_2nd	e6juyC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: COG1915_2nd	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.75.10.10	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (utative)
D	3.40.50.10690	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	putative lor/sdh protein like domains	CATH (utative)
A	3.75.10.10	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (utative)
A	3.40.50.10690	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	putative lor/sdh protein like domains	CATH (utative)
C	3.75.10.10	Alpha Beta	5-stranded Propeller	L-arginine/glycine Amidinotransferase	Chain A	CATH (utative)
C	3.40.50.10690	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	putative lor/sdh protein like domains	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF21570	Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold (ArgZ-like_C_2nd)	Arginine dihydrolase ArgZ-like, C-terminal, Rossmann fold	This domain is found at the C-terminal end of Arginine dihydrolase ArgZ from Synechocystis sp (also known as Sll1336 protein) and similar prokaryotic sequences. ArgZ is involved in an ornithine- ammonia cycle (OAC) in cyanobacteria, which confers sub ...	This domain is found at the C-terminal end of Arginine dihydrolase ArgZ from Synechocystis sp (also known as Sll1336 protein) and similar prokaryotic sequences. ArgZ is involved in an ornithine- ammonia cycle (OAC) in cyanobacteria, which confers substantial adaptability under environmental nitrogen fluctuations. This protein is organised into three domains: a N-terminal domain belonging to the guanidino group-modifying enzyme (GME) family, a middle oxoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme (Pfam:PF04455) and a C-terminal uncharacterized region that can be divided in two subdomains. This entry represents the most C-terminal region, which forms a large Rossmann fold domain. Its specific function is unknown [1].	Domain
A, B, C, D	PF19420	N,N dimethylarginine dimethylhydrolase, eukaryotic (DDAH_eukar)	N,N dimethylarginine dimethylhydrolase, eukaryotic	-	Family
A, B, C, D	PF21571	Arginine dihydrolase ArgZ-like, C-terminal, first region (ArgZ-like_C_1st)	Arginine dihydrolase ArgZ-like, C-terminal, first region	This domain is found at the C-terminal end of Arginine dihydrolase ArgZ from Synechocystis sp (also known as Sll1336 protein) and similar prokaryotic sequences. ArgZ is involved in an ornithine- ammonia cycle (OAC) in cyanobacteria, which confers sub ...	This domain is found at the C-terminal end of Arginine dihydrolase ArgZ from Synechocystis sp (also known as Sll1336 protein) and similar prokaryotic sequences. ArgZ is involved in an ornithine- ammonia cycle (OAC) in cyanobacteria, which confers substantial adaptability under environmental nitrogen fluctuations. This protein is organised into three domains: a N-terminal domain belonging to the guanidino group-modifying enzyme (GME) family, a middle oxoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme (Pfam:PF04455) and a C-terminal uncharacterized region that can be divided in two subdomains. This entry represents the small first region of the C-terminal domain, which folds into beta-strands. Its specific function is unknown [1].	Domain
A, B, C, D	PF04455	LOR/SDH bifunctional enzyme conserved region (Saccharop_dh_N)	LOR/SDH bifunctional enzyme conserved region	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Sll1336 protein	hydrolase activity catalytic activity lyase activity binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR048964	Arginine dihydrolase ArgZ/ArgE-like, C-terminal, first subdomain	Domain
A, B, C, D	IPR005239	Bifunctional arginine dihydrolase/ornithine cyclodeaminase ArgZ/ArgE-like	Family
A, B, C, D	IPR048963	Arginine dihydrolase ArgZ/ArgE-like, C-terminal, second subdomain	Domain
A, B, C, D	IPR007545	LOR/SDH bifunctional enzyme, conserved domain	Domain
A, B, C, D	IPR029035	DHS-like NAD/FAD-binding domain 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.