2DER | pdb_00002der

Cocrystal structure of an RNA sulfuration enzyme MnmA and tRNA-Glu in the initial tRNA binding state

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)
D [auth B]	SCOP2B Superfamily	GS N-terminal domain-like	8051820	3000408	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	EF-Tu post-G domain-like	8051819	3002024	SCOP2B (2022-06-29)
D [auth B]	SCOP2B Superfamily	Nucleotidylyl transferase	8051816	3001541	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	Nucleotidylyl transferase	8051816	3001541	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	EF-Tu post-G domain-like	8051819	3002024	SCOP2B (2022-06-29)
C [auth A]	SCOP2B Superfamily	GS N-terminal domain-like	8051820	3000408	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)
D [auth B]	PTS_EIIB	e2derB2	A: alpha bundles	X: Fusion glycoprotein F2	H: HTH	T: winged helix domain	F: PTS_EIIB	ECOD (develop294)
C [auth A]	zf-CCCH	e2derA1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: zf-CCCH	ECOD (develop294)
C [auth A]	Lipoprotein_1	e2derA2	A: alpha bundles	X: HAMP domain	H: HAMP domain	T: HAMP domain	F: Lipoprotein_1	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
D [auth B]	2.30.30.280	Mainly Beta	Roll	SH3 type barrels.	Adenine nucleotide alpha hydrolases-like domains	CATH (4.3.0)
D [auth B]	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C [auth A]	3.40.50.620	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	HUPs	CATH (4.3.0)
C [auth A]	2.30.30.280	Mainly Beta	Roll	SH3 type barrels.	Adenine nucleotide alpha hydrolases-like domains	CATH (4.3.0)
C [auth A]	2.40.30.10	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A], D [auth B]	PF03054	tRNA methyl transferase HUP domain (tRNA_Me_trans)	tRNA methyl transferase HUP domain	This family represents the N-terminal HUP domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tR ...	This family represents the N-terminal HUP domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs [1].	Domain
C [auth A], D [auth B]	PF20258	Aminomethyltransferase beta-barrel domain (tRNA_Me_trans_C)	Aminomethyltransferase beta-barrel domain	This domain is found at the C-terminus of tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs [1].	Domain
C [auth A], D [auth B]	PF20259	tRNA methyl transferase PRC-barrel domain (tRNA_Me_trans_M)	tRNA methyl transferase PRC-barrel domain	This family represents a central PRC-barrel domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some ...	This family represents a central PRC-barrel domain in tRNA(5-methylaminomethyl-2-thiouridine)-methyltransferase which is involved in the biosynthesis of the modified nucleoside 5-methylaminomethyl-2-thiouridine present in the wobble position of some tRNAs [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A], D [auth B]	tRNA-specific 2-thiouridylase mnmA	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 sulfurtransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity RNA binding tRNA binding nucleic acid binding tRNA-uridine 2-sulfurtransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid catalytic activity, acting on a tRNA	response to acid chemical response to stimulus response to chemical response to stress stress response to acid chemical 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 response to acid chemical response to stimulus response to chemical response to stress stress response to acid chemical 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
A [auth C], B [auth D]	tRNA	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A], D [auth B]	IPR004506	tRNA-specific 2-thiouridylase MnmA-like	Family
C [auth A], D [auth B]	IPR046885	tRNA-specific 2-thiouridylase MnmA-like, C-terminal domain	Domain
C [auth A], D [auth B]	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold	Homologous Superfamily
C [auth A], D [auth B]	IPR023382	tRNA-specific 2-thiouridylase MnmA-like, central domain superfamily	Homologous Superfamily
C [auth A], D [auth B]	IPR046884	tRNA-specific 2-thiouridylase MnmA-like, central domain	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.