5XDA | pdb_00005xda

Structural basis for Ufm1 recognition by UfSP

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)
L	SCOP2B Superfamily	Ubiquitin-like	8041140	3000157	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ubiquitin-like	8041140	3000157	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ubiquitin-like	8041140	3000157	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ubiquitin-like	8041140	3000157	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ubiquitin-like	8041140	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8041140	3000157	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)
L	Ufm1	e5xdaL1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ufm1	ECOD (1.6)
K	Ufm1	e5xdaK1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ufm1	ECOD (1.6)
J	Ufm1	e5xdaJ1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ufm1	ECOD (1.6)
I	Ufm1	e5xdaI1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ufm1	ECOD (1.6)
H	Ufm1	e5xdaH1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ufm1	ECOD (1.6)
G	Ufm1	e5xdaG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Ufm1	ECOD (1.6)
F	KOG2433	e5xdaF1	A: a+b two layers	X: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	H: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	T: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2	F: KOG2433	ECOD (1.6)
F	KOG2433_1	e5xdaF2	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: KOG2433_1	ECOD (1.6)
F	Peptidase_C78	e5xdaF3	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C78	ECOD (1.6)
E	KOG2433	e5xdaE2	A: a+b two layers	X: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	H: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	T: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2	F: KOG2433	ECOD (1.6)
E	KOG2433_1	e5xdaE1	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: KOG2433_1	ECOD (1.6)
E	Peptidase_C78	e5xdaE3	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C78	ECOD (1.6)
D	KOG2433	e5xdaD1	A: a+b two layers	X: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	H: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	T: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2	F: KOG2433	ECOD (1.6)
D	KOG2433_1	e5xdaD2	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: KOG2433_1	ECOD (1.6)
D	Peptidase_C78	e5xdaD3	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C78	ECOD (1.6)
C	KOG2433	e5xdaC3	A: a+b two layers	X: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	H: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	T: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2	F: KOG2433	ECOD (1.6)
C	KOG2433_1	e5xdaC2	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: KOG2433_1	ECOD (1.6)
C	Peptidase_C78	e5xdaC1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C78	ECOD (1.6)
B	KOG2433	e5xdaB2	A: a+b two layers	X: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	H: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	T: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2	F: KOG2433	ECOD (1.6)
B	KOG2433_1	e5xdaB3	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: KOG2433_1	ECOD (1.6)
B	Peptidase_C78	e5xdaB1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C78	ECOD (1.6)
A	KOG2433	e5xdaA1	A: a+b two layers	X: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	H: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 (From Topology)	T: N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2	F: KOG2433	ECOD (1.6)
A	KOG2433_1	e5xdaA2	A: a+b three layers	X: Cytidine deaminase-like (From Topology)	H: Cytidine deaminase-like (From Topology)	T: Cytidine deaminase-like	F: KOG2433_1	ECOD (1.6)
A	Peptidase_C78	e5xdaA3	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: Peptidase_C78	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
K	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
J	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
I	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
H	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
G	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
F	3.90.70.130	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (utative)
E	3.90.70.130	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (utative)
D	3.90.70.130	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (utative)
C	3.90.70.130	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (utative)
B	3.90.70.130	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (utative)
A	3.90.70.130	Alpha Beta	Alpha-Beta Complex	Cathepsin B	Chain A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G, H, I, J, K G, H, I, J, K, L	PF03671	Ubiquitin fold modifier 1 protein (Ufm1)	Ubiquitin fold modifier 1 protein	This is a family of short ubiquitin-like proteins, that is like neither type-1 or type-2. It is a ubiquitin-fold modifier 1 (Ufm1) that is synthesised in a precursor form of 85 amino-acid residues. In humans the enzyme for Ufm1 is Uba5 and the conjug ...	This is a family of short ubiquitin-like proteins, that is like neither type-1 or type-2. It is a ubiquitin-fold modifier 1 (Ufm1) that is synthesised in a precursor form of 85 amino-acid residues. In humans the enzyme for Ufm1 is Uba5 and the conjugating enzyme is Ufc1. Prior to activation by Uba5 the extra two amino acids at the C-terminal region of the human pro-Ufm1 protein are removed to expose Gly whose residue is necessary for conjugation to target molecule(s). The mature Ufm1 is conjugated to yet unidentified endogenous proteins,[1]. While Ubiquitin and many Ubls possess the conserved C-terminal di-glycine that is adenylated by each specific E1 or E1-like enzyme, respectively, in an ATP-dependent manner, Ufm1(1-83) possesses a single glycine at its C-terminus, which is followed by a Ser-Cys dipeptide in the precursor form of Ufm1. The C-terminally processed Ufm1(1-83) is specifically activated by Uba5, an E1-like enzyme, and then transferred to its cognate Ufc1, an E2-like enzyme [2].	Domain
A, B, C, D, E A, B, C, D, E, F	PF20908	Ubiquitin-fold modifier 1 specific protease 2, N-terminal (UfSP2_N)	Ubiquitin-fold modifier 1 specific protease 2, N-terminal	This domain is found at the N-terminal end of the eukaryotic protein Ubiquitin-fold modifier 1 (Ufm1) specific protease 2 (UfSP2). UfSP2 is a cysteine protease which recognises and hydrolyses the peptide bond at the C-terminal Gly residue of the prot ...	This domain is found at the N-terminal end of the eukaryotic protein Ubiquitin-fold modifier 1 (Ufm1) specific protease 2 (UfSP2). UfSP2 is a cysteine protease which recognises and hydrolyses the peptide bond at the C-terminal Gly residue of the protein Ufm1, a ubiquitin- like modifier. This protein is organised into two domains: the catalytic C-terminal (Pfam:PF07910) and a N-terminal showing a six- stranded beta-sheet with five helices. This entry represents the most N-terminal beta-strand [1,2].	Domain
A, B, C, D, E A, B, C, D, E, F	PF22084	Ufm1 specific protease UfSP N-terminal MPN domain (UfSP_MPN_N)	Ufm1 specific protease UfSP N-terminal MPN domain	UfSP is a cysteine protease that activates Ufm1 from its precursor by processing the C-terminus to expose the conserved Gly necessary for substrate conjugation and de-conjugates Ufm1 from the substrate. UfSP from C. elegans consists of three domains: ...	UfSP is a cysteine protease that activates Ufm1 from its precursor by processing the C-terminus to expose the conserved Gly necessary for substrate conjugation and de-conjugates Ufm1 from the substrate. UfSP from C. elegans consists of three domains: MPN domain, N-domain and a catalytic domain. This entry represents the MPN domain that forms an alpha/beta globular structure with a central mixed beta-sheet packed on both sides with helices and a pair of two strands and a helix. This domain modulates both substrate recognition and deufmylation activity [1-2].	Domain
A, B, C, D, E A, B, C, D, E, F	PF07910	Peptidase family C78 (Peptidase_C78)	Peptidase family C78	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I, J, K G, H, I, J, K, L	Ubiquitin-fold modifier 1	-	primary metabolic process protein ufmylation macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process macroautophagy reticulophagy primary metabolic process protein ufmylation macromolecule modification metabolic process cellular process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal catabolic process macroautophagy reticulophagy autophagy process utilizing autophagic mechanism cellular response to stimulus cellular response to stress response to stimulus response to stress response to endoplasmic reticulum stress	cellular anatomical structure intracellular anatomical structure cytoplasm membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle
A, B, C, D, E A, B, C, D, E, F	Ufm1-specific protease	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity deUFMylase activity catalytic activity	chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion positive regulation of locomotion regulation of biological process regulation of response to external stimulus biological regulation positive regulation of biological process regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus chemotaxis response to stimulus taxis response to chemical response to external stimulus locomotion positive regulation of locomotion regulation of biological process regulation of response to external stimulus biological regulation positive regulation of biological process regulation of chemotaxis positive regulation of chemotaxis positive regulation of response to stimulus positive regulation of response to external stimulus regulation of response to stimulus regulation of locomotion localization protein localization to cilium protein localization to organelle macromolecule localization intracellular protein localization protein localization to non-motile cilium proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process response to alcohol response to oxygen-containing compound response to ethanol	cellular anatomical structure intracellular anatomical structure perinuclear region of cytoplasm cytoplasm protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle endoplasmic reticulum endomembrane system organelle subcompartment membrane cellular anatomical structure intracellular anatomical structure perinuclear region of cytoplasm cytoplasm protein-containing complex membrane-bounded organelle intracellular organelle organelle nucleus intracellular membrane-bounded organelle endoplasmic reticulum endomembrane system organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H, I, J, K G, H, I, J, K, L	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
G, H, I, J, K G, H, I, J, K, L	IPR005375	Ubiquitin-fold modifier 1	Family
A, B, C, D, E A, B, C, D, E, F	IPR049387	Ubiquitin-fold modifier 1 specific protease 2-like, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR012462	UfSP1/2/DUB, catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR054308	Ufm1-specific protease, MPN domain	Domain