4RT0 | pdb_00004rt0

Structure of the Alg44 PilZ domain from Pseudomonas aeruginosa PAO1 in complex 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)
C	SCOP2B Superfamily	PilZ domain-like	8091597	3000480	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	PilZ domain-like	8091597	3000480	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PilZ domain-like	8091597	3000480	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)
C	N6_Mtase	e4rt0C1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (develop294)
B	N6_Mtase	e4rt0B1	A: alpha bundles	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (develop294)
A	Lipocalin	e4rt0A1	A: alpha bundles	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: Lipocalin	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.40.10.220	Mainly Beta	Beta Barrel	Thrombin, subunit H	predicted glycosyltransferase like domains	CATH (4.3.0)
B	2.40.10.220	Mainly Beta	Beta Barrel	Thrombin, subunit H	predicted glycosyltransferase like domains	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, B, C	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Alginate biosynthesis protein Alg44	CoA-ligase activity fatty acid ligase activity long-chain fatty acid-CoA ligase activity ligase activity, forming carbon-sulfur bonds fatty acid-CoA ligase activity catalytic activity acid-thiol ligase activity ligase activity ATP-dependent activity guanyl nucleotide binding binding cyclic nucleotide binding nucleotide binding guanyl ribonucleotide binding CoA-ligase activity fatty acid ligase activity long-chain fatty acid-CoA ligase activity ligase activity, forming carbon-sulfur bonds fatty acid-CoA ligase activity catalytic activity acid-thiol ligase activity ligase activity ATP-dependent activity 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 lipid transporter activity lipid transmembrane transporter activity transporter activity monocarboxylic acid transmembrane transporter activity carboxylic acid transmembrane transporter activity transmembrane transporter activity bile acid transmembrane transporter activity glycosyltransferase activity alginate synthase activity transferase activity hexosyltransferase activity	carbohydrate metabolic process alginic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process carboxylic acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process macromolecule biosynthetic process carboxylic acid biosynthetic process polysaccharide metabolic process biosynthetic process carbohydrate metabolic process alginic acid biosynthetic process small molecule biosynthetic process oxoacid metabolic process polysaccharide biosynthetic process carbohydrate biosynthetic process carboxylic acid metabolic process primary metabolic process organic acid biosynthetic process organic acid metabolic process macromolecule biosynthetic process carboxylic acid biosynthetic process polysaccharide metabolic process biosynthetic process small molecule metabolic process metabolic process cellular process macromolecule metabolic process organic anion transport carboxylic acid transport transport lipid localization bile acid and bile salt transport lipid transport organic hydroxy compound transport establishment of localization organic acid transport localization monocarboxylic acid transport macromolecule localization cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms single-species biofilm formation aggregation of unicellular organisms xenobiotic export from cell xenobiotic transport response to stimulus xenobiotic detoxification by transmembrane export across the plasma membrane detoxification export from cell export across plasma membrane response to toxic substance transmembrane transport response to chemical	cell periphery cellular anatomical structure plasma membrane membrane periplasmic space Gram-negative-bacterium-type cell wall external encapsulating structure cell envelope cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR009875	PilZ domain	Domain
A, B, C	IPR050739	Membrane Fusion Protein	Family
A, B, C	IPR058835	ALG44, barrel-sandwich hybrid domain	Domain
A, B, C	IPR058833	ALG44, helical loop domain	Domain
A, B, C	IPR058834	ALG44, beta-barrel 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.