2D1P | pdb_00002d1p

crystal structure of heterohexameric TusBCD proteins, which are crucial for the tRNA modification

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
G	d2d1pg2	Alpha and beta proteins (a/b)	DsrEFH-like	DsrEFH-like	DsrEF-like	tRNA 2-thiouridine synthesizing protein D, TusD	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G	d2d1pg3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2d1pd2	Alpha and beta proteins (a/b)	DsrEFH-like	DsrEFH-like	DsrEF-like	tRNA 2-thiouridine synthesizing protein D, TusD	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
D	d2d1pd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2d1pa1	Alpha and beta proteins (a/b)	DsrEFH-like	DsrEFH-like	DsrEF-like	tRNA 2-thiouridine synthesizing protein D, TusD	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
A	d2d1pa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H	d2d1ph_	Alpha and beta proteins (a/b)	DsrEFH-like	DsrEFH-like	DsrEF-like	tRNA 2-thiouridine synthesizing protein C, TusC	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
E	d2d1pe_	Alpha and beta proteins (a/b)	DsrEFH-like	DsrEFH-like	DsrEF-like	tRNA 2-thiouridine synthesizing protein C, TusC	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
B	d2d1pb1	Alpha and beta proteins (a/b)	DsrEFH-like	DsrEFH-like	DsrEF-like	tRNA 2-thiouridine synthesizing protein C, TusC	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I	d2d1pi_	Alpha and beta proteins (a/b)	DsrEFH-like	DsrEFH-like	DsrH-like	tRNA 2-thiouridine synthesizing protein B, TusB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
F	d2d1pf_	Alpha and beta proteins (a/b)	DsrEFH-like	DsrEFH-like	DsrH-like	tRNA 2-thiouridine synthesizing protein B, TusB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
C	d2d1pc1	Alpha and beta proteins (a/b)	DsrEFH-like	DsrEFH-like	DsrH-like	tRNA 2-thiouridine synthesizing protein B, TusB	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G	SCOP2B Superfamily	DsrEFH-like	8039496	3001075	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DsrEFH-like	8039496	3001075	SCOP2B (2022-06-29)
A	SCOP2 Family	DsrEF-like	8027117	4002297	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	DsrEFH-like	8039496	3001075	SCOP2 (2022-06-29)
H	SCOP2B Superfamily	DsrEFH-like	8039499	3001075	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DsrEFH-like	8039499	3001075	SCOP2B (2022-06-29)
B	SCOP2 Family	DsrEF-like	8027120	4002297	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	DsrEFH-like	8039499	3001075	SCOP2 (2022-06-29)
I	SCOP2B Superfamily	DsrEFH-like	8039500	3001075	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DsrEFH-like	8039500	3001075	SCOP2B (2022-06-29)
C	SCOP2 Family	DsrH-like	8027121	4003397	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	DsrEFH-like	8039500	3001075	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G	DrsE	e2d1pG1	A: a/b three-layered sandwiches	X: YchN-like (From Topology)	H: YchN-like (From Topology)	T: YchN-like	F: DrsE	ECOD (1.6)
D	DrsE	e2d1pD1	A: a/b three-layered sandwiches	X: YchN-like (From Topology)	H: YchN-like (From Topology)	T: YchN-like	F: DrsE	ECOD (1.6)
A	DrsE	e2d1pA1	A: a/b three-layered sandwiches	X: YchN-like (From Topology)	H: YchN-like (From Topology)	T: YchN-like	F: DrsE	ECOD (1.6)
H	DrsE	e2d1pH1	A: a/b three-layered sandwiches	X: YchN-like (From Topology)	H: YchN-like (From Topology)	T: YchN-like	F: DrsE	ECOD (1.6)
E	DrsE	e2d1pE1	A: a/b three-layered sandwiches	X: YchN-like (From Topology)	H: YchN-like (From Topology)	T: YchN-like	F: DrsE	ECOD (1.6)
B	DrsE	e2d1pB1	A: a/b three-layered sandwiches	X: YchN-like (From Topology)	H: YchN-like (From Topology)	T: YchN-like	F: DrsE	ECOD (1.6)
I	DsrH	e2d1pI1	A: a/b three-layered sandwiches	X: YchN-like (From Topology)	H: YchN-like (From Topology)	T: YchN-like	F: DsrH	ECOD (1.6)
F	DsrH	e2d1pF1	A: a/b three-layered sandwiches	X: YchN-like (From Topology)	H: YchN-like (From Topology)	T: YchN-like	F: DsrH	ECOD (1.6)
C	DsrH	e2d1pC1	A: a/b three-layered sandwiches	X: YchN-like (From Topology)	H: YchN-like (From Topology)	T: YchN-like	F: DsrH	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	3.40.1260.10	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
D	3.40.1260.10	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
A	3.40.1260.10	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
H	3.40.1260.10	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
E	3.40.1260.10	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
B	3.40.1260.10	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
I	3.40.1260.10	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
F	3.40.1260.10	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)
C	3.40.1260.10	Alpha Beta	3-Layer(aba) Sandwich	Hypothetical Protein Ychn	Chain: A,	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D, G	PF02635	DsrE/DsrF-like family (DsrE)	DsrE/DsrF-like family	DsrE is a small soluble protein involved in intracellular sulfur reduction [1]. This family also includes DsrF and the homologues TusD/C. n E. coli, the DsrEFH homologue TusBCD interacts with the DsrC homologue TusE in a sulfur relay system during 2- ...	DsrE is a small soluble protein involved in intracellular sulfur reduction [1]. This family also includes DsrF and the homologues TusD/C. n E. coli, the DsrEFH homologue TusBCD interacts with the DsrC homologue TusE in a sulfur relay system during 2-thiouridine biosynthesis [2].	Domain
B, E, H	PF02635	DsrE/DsrF-like family (DsrE)	DsrE/DsrF-like family	DsrE is a small soluble protein involved in intracellular sulfur reduction [1]. This family also includes DsrF and the homologues TusD/C. n E. coli, the DsrEFH homologue TusBCD interacts with the DsrC homologue TusE in a sulfur relay system during 2- ...	DsrE is a small soluble protein involved in intracellular sulfur reduction [1]. This family also includes DsrF and the homologues TusD/C. n E. coli, the DsrEFH homologue TusBCD interacts with the DsrC homologue TusE in a sulfur relay system during 2-thiouridine biosynthesis [2].	Domain
C, F, I	PF04077	DsrH like protein (DsrH)	DsrH like protein	DsrH is involved in oxidation of intracellular sulphur in the phototrophic sulphur bacterium Chromatium vinosum D [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D, G	Hypothetical UPF0163 protein yheN	sulfur carrier activity molecular carrier activity sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity	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 primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process 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 primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process tRNA wobble position uridine thiolation	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex catalytic complex sulfurtransferase complex transferase complex
B, E, H	Hypothetical UPF0116 protein yheM	-	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 primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process 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 primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process tRNA wobble position uridine thiolation	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex sulfurtransferase complex transferase complex cytoplasm cytosol
C, F, I	Hypothetical protein yheL	-	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 primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process 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 primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process tRNA metabolic process RNA modification biosynthetic process macromolecule modification metabolic process cellular process macromolecule metabolic process tRNA wobble position uridine thiolation	protein-containing complex cellular anatomical structure intracellular anatomical structure catalytic complex sulfurtransferase complex transferase complex cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D, G	IPR027396	DsrEFH-like	Homologous Superfamily
A, D, G	IPR017463	Sulphur relay, TusD/DsrE	Family
A, D, G	IPR003787	Sulphur relay, DsrE/F-like	Family
B, E, H	IPR027396	DsrEFH-like	Homologous Superfamily
B, E, H	IPR037450	Sulphur relay, TusC	Family
B, E, H	IPR003787	Sulphur relay, DsrE/F-like	Family
B, E, H	IPR017462	Sulphur relay, TusC/DsrF	Family
C, F, I	IPR007215	Sulphur relay, TusB/DsrH	Family
C, F, I	IPR027396	DsrEFH-like	Homologous Superfamily
C, F, I	IPR023526	Sulphur relay, TusB	Family

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.