6Z6S

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)
A [auth DDD]	PF00899	e6z6sDDD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: Activating enzymes of the ubiquitin-like proteins	F: PF00899	ECOD (1.6)
B [auth GGG]	PF09138	e6z6sGGG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF09138	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	Homologous Superfamily
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

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.