3MK5

Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase domain from Mycobacterium tuberculosis with sulfate and zinc at pH 4.00

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)
A	d3mk5a1	Alpha and beta proteins (a+b)	YrdC/RibB	YrdC/RibB	automated matches	automated matches	(Mycobacterium tuberculosis H37Ra ) [TaxId: 419947 ],	SCOPe (2.08)
A	d3mk5a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis H37Ra ) [TaxId: 419947 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	YrdC/RibB-like	8074994	3000166	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	DHBP_synthase	e3mk5A1	A: a+b complex topology	X: YrdC/RibB (From Topology)	H: YrdC/RibB (From Topology)	T: YrdC/RibB	F: DHBP_synthase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.870.10	Alpha Beta	Alpha-Beta Complex	DHBP synthase	DHBP synthase	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00926	3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBP_synthase)	3,4-dihydroxy-2-butanone 4-phosphate synthase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	3,4-dihydroxy-2-butanone 4-phosphate synthase	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding lyase activity catalytic activity 3,4-dihydroxy-2-butanone-4-phosphate synthase activity carbon-carbon lyase activity manganese ion binding transition metal ion binding zinc ion binding guanyl nucleotide binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding lyase activity catalytic activity 3,4-dihydroxy-2-butanone-4-phosphate synthase activity carbon-carbon lyase activity manganese ion binding transition metal ion binding zinc ion binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines GTP cyclohydrolase II activity GTP cyclohydrolase activity cyclohydrolase activity hydrolase activity hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	organonitrogen compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular biosynthetic process flavin-containing compound metabolic process cellular metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process organic cyclic compound metabolic process flavin-containing compound biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organonitrogen compound metabolic process water-soluble vitamin biosynthetic process small molecule biosynthetic process cellular biosynthetic process flavin-containing compound metabolic process cellular metabolic process organonitrogen compound biosynthetic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process organic cyclic compound metabolic process flavin-containing compound biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process small molecule metabolic process cellular process water-soluble vitamin metabolic process riboflavin metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR000422	3,4-dihydroxy-2-butanone 4-phosphate synthase, RibB	Family
A	IPR032677	GTP cyclohydrolase II	Domain
A	IPR016299	Riboflavin biosynthesis protein RibBA	Family
A	IPR017945	DHBP synthase RibB-like alpha/beta domain superfamily	Homologous Superfamily
A	IPR000926	GTP cyclohydrolase II, RibA	Family
A	IPR036144	GTP cyclohydrolase II superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.