5SXY

The solution NMR structure for the PqqD truncation of Methylobacterium extorquens PqqCD representing a functional and stand-alone ribosomally synthesized and post-translational modified (RiPP) recognition element (RRE)

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)
A	SCOP2 Family	PqqD-like	8087363	4005476	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Winged helix DNA-binding domain	8090246	3000034	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)
A	PF05402	e5sxyA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF05402	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF05402	Coenzyme PQQ synthesis protein D (PqqD) (PqqD)	Coenzyme PQQ synthesis protein D (PqqD)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Bifunctional coenzyme PQQ synthesis protein C/D	pyrroloquinoline-quinone synthase activity oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor binding quinone binding small molecule binding	pyrroloquinoline quinone biosynthetic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process cellular ketone metabolic process organic substance biosynthetic process small molecule metabolic process tricarboxylic acid biosynthetic process organonitrogen compound metabolic process tricarboxylic acid metabolic process pyrroloquinoline quinone biosynthetic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process organic substance metabolic process cellular ketone metabolic process organic substance biosynthetic process small molecule metabolic process tricarboxylic acid biosynthetic process organonitrogen compound metabolic process tricarboxylic acid metabolic process small molecule biosynthetic process cellular metabolic process carboxylic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process ketone biosynthetic process sulfur compound metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004305	Thiaminase-2/PQQC	Domain
A	IPR039068	Pyrroloquinoline-quinone synthase-like	Family
A	IPR022479	Coenzyme PQQ synthesis D, bacteria	Family
A	IPR008792	Coenzyme PQQ synthesis protein D	Family
A	IPR041881	Coenzyme PQQ synthesis protein D superfamily	Homologous Superfamily
A	IPR011845	Coenzyme PQQ biosynthesis protein C	Family
A	IPR016084	Haem oxygenase-like, multi-helical	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.