3KYF

Crystal structure of P4397 complexed with c-di-GMP

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)
A	SCOP2 Family	PilZ domain-associated domain	8049309	4001875	SCOP2 (2022-06-29)
A	SCOP2 Family	PilZ domain-like	8091579	4001865	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PilZ domain-like	8091580	3000480	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PilZ domain-like	8091581	3000480	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	PilZ	e3kyfA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: PilZ	ECOD (1.6)
A	YcgR	e3kyfA2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: YcgR	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
A	2.40.10.220	Mainly Beta	Beta Barrel	Thrombin, subunit H	predicted glycosyltransferase like domains	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF07238	PilZ domain (PilZ)	PilZ domain	PilZ is a c-di-GMP binding domain [3] found in widespread cytoplasmic receptors, which is involved in regulation of motility, biofilm formation and virulence of many bacterial pathogens. This domain binds c-di-GMP through RXXXR and [D/N]hSXXG motifs, ...	PilZ is a c-di-GMP binding domain [3] found in widespread cytoplasmic receptors, which is involved in regulation of motility, biofilm formation and virulence of many bacterial pathogens. This domain binds c-di-GMP through RXXXR and [D/N]hSXXG motifs, however, some PilZ domains lack these motifs and do not bind c-di-GMP [6]. Proteins which contain PilZ are known to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias [5]. This is the canonical PilZ domain whose structure consists of six beta-strands that form a beta barrel, followed by a long C-terminal alpha-helix [6].	Domain
A	PF07317	Flagellar regulator YcgR, PilZN domain (PilZN)	Flagellar regulator YcgR, PilZN domain	This domain is found N terminal to Pfam:PF07238, therefore named PilZN. Proteins which contain PilZN (also known as YcgR) are know to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque ...	This domain is found N terminal to Pfam:PF07238, therefore named PilZN. Proteins which contain PilZN (also known as YcgR) are know to interact with the flagellar switch-complex proteins FliG and FliM. This interaction results in a reduction of torque generation and induces CCW motor bias [3]. This domain exhibits a similar structur as PilZ domains comprising a beta-barrel fold but lack the C-terminal alpha-helix [4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Putative uncharacterized protein	guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding cyclic-di-GMP binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding nucleoside phosphate binding ion binding cyclic-di-GMP binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	bacterial-type flagellum-dependent cell motility cellular process cell motility archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility regulation of bacterial-type flagellum-dependent cell motility regulation of biological process regulation of cell motility regulation of cellular process biological regulation regulation of bacterial-type flagellum-dependent cell motility by regulation of motor speed regulation of locomotion locomotion	bacterial-type flagellum basal body cell projection cellular anatomical structure organelle membraneless organelle bacterial-type flagellum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR012349	FMN-binding split barrel	Homologous Superfamily
A	IPR009926	Type III secretion system flagellar brake protein YcgR, PilZN domain	Domain
A	IPR009875	PilZ domain	Domain
A	IPR023787	Type III secretion system flagellar brake protein YcgR	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.