6Z6S | pdb_00006z6s

Crystal structure of Uba4-Urm1 from Chaetomium thermophilum

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
B [auth GGG]	SCOP2B Superfamily	MoaD/ThiS-like	8097796	3000330	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)
B [auth GGG]	Urm1	e6z6sGGG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Urm1	ECOD (1.6)
A [auth DDD]	ThiF_1	e6z6sDDD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: ThiF_1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth GGG]	PF09138	Urm1 (Ubiquitin related modifier) (Urm1)	Urm1 (Ubiquitin related modifier)	Urm1 is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like pathway urmylation [1]. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and ...	Urm1 is a ubiquitin related protein that modifies proteins in the yeast ubiquitin-like pathway urmylation [1]. Structural comparisons and phylogenetic analysis of the ubiquitin superfamily has indicated that Urm1 has the most conserved structural and sequence features of the common ancestor of the entire superfamily [2].	Domain
A [auth DDD]	PF00899	ThiF family (ThiF)	ThiF family	This domain is found in ubiquitin activating E1 family and members of the bacterial ThiF/MoeB/HesA family. It is repeated in Ubiquitin-activating enzyme E1 [1-3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth GGG]	Ubiquitin-related modifier 1	cation binding ion binding binding metal ion binding small molecule binding	primary metabolic process protein urmylation 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 tRNA thio-modification tRNA modification RNA metabolic process primary metabolic process protein urmylation 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 tRNA thio-modification tRNA modification RNA metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process RNA modification biosynthetic process tRNA processing RNA processing tRNA wobble uridine modification tRNA wobble base modification	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
A [auth DDD]	Adenylyltransferase and sulfurtransferase uba4	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding adenylyltransferase activity molybdopterin-synthase adenylyltransferase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups thiosulfate-cyanide sulfurtransferase activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups molybdopterin-synthase sulfurtransferase activity cation binding metal ion binding ubiquitin-like modifier activating enzyme activity ligase activity, forming carbon-sulfur bonds catalytic activity, acting on a protein URM1 activating enzyme activity ligase activity ATP-dependent activity	primary metabolic process protein urmylation 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 tRNA thio-modification RNA metabolic process tRNA wobble uridine modification primary metabolic process protein urmylation 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 tRNA thio-modification RNA metabolic process tRNA wobble uridine modification nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process tRNA processing tRNA wobble base modification RNA processing tRNA modification gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process RNA modification biosynthetic process tRNA wobble position uridine thiolation Mo-molybdopterin cofactor biosynthetic process Mo-molybdopterin cofactor metabolic process prosthetic group metabolic process molybdopterin cofactor biosynthetic process organophosphate metabolic process organophosphate biosynthetic process molybdopterin cofactor metabolic process phosphate-containing compound metabolic process phosphorus metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth GGG]	IPR015221	Ubiquitin-related modifier 1	Family
B [auth GGG]	IPR016155	Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp	Homologous Superfamily
B [auth GGG]	IPR012675	Beta-grasp domain superfamily	Homologous Superfamily
A [auth DDD]	IPR001763	Rhodanese-like domain	Domain
A [auth DDD]	IPR036873	Rhodanese-like domain superfamily	Homologous Superfamily
A [auth DDD]	IPR045886	ThiF/MoeB/HesA family	Family
A [auth DDD]	IPR000594	THIF-type NAD/FAD binding fold	Domain
A [auth DDD]	IPR028885	Adenylyltransferase and sulfurtransferase MOCS3/Uba4	Family
A [auth DDD]	IPR035985	Ubiquitin-activating enzyme-like	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.