Annotations: 4H54

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CZB	e4h54A2	A: alpha bundles	X: Four-helical up-and-down bundle	H: Regulatory CZB domain of diguanylate cyclase YdeH (From Topology)	T: Regulatory CZB domain of diguanylate cyclase YdeH	F: CZB	ECOD (1.6)
A	GGDEF	e4h54A1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: GGDEF	ECOD (1.6)
B	CZB	e4h54B2	A: alpha bundles	X: Four-helical up-and-down bundle	H: Regulatory CZB domain of diguanylate cyclase YdeH (From Topology)	T: Regulatory CZB domain of diguanylate cyclase YdeH	F: CZB	ECOD (1.6)
B	GGDEF	e4h54B1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: GGDEF	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.30	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Aspartate receptor, ligand-binding domain	CATH (4.3.0)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)
B	1.20.120.30	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Aspartate receptor, ligand-binding domain	CATH (4.3.0)
B	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00990	Diguanylate cyclase, GGDEF domain (GGDEF)	Diguanylate cyclase, GGDEF domain	This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain [1] and has diguanylate cyclase activity [4]. This observation correlates with ...	This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain [1] and has diguanylate cyclase activity [4]. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. In the WspR protein of Pseudomonas aeruginosa, the GGDEF domain acts as a diguanylate cyclase, PDB:3bre, when the whole molecule appears to form a tetramer consisting of two symmetrically-related dimers representing a biological unit. The active site is the GGD/EF motif, buried in the structure, and the cyclic dimeric guanosine monophosphate (c-di-GMP) bind to the inhibitory-motif RxxD on the surface. The enzyme thus catalyses the cyclisation of two guanosine triphosphate (GTP) molecules to one c-di-GMP molecule [6,7,8].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Diguanylate cyclase YdeH	transferase activity nucleotidyltransferase activity catalytic activity diguanylate cyclase activity transferase activity, transferring phosphorus-containing groups identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding transferase activity nucleotidyltransferase activity catalytic activity diguanylate cyclase activity transferase activity, transferring phosphorus-containing groups identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule 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	regulation of biological process cell aggregation regulation of cellular process biofilm formation regulation of single-species biofilm formation on inanimate substrate positive regulation of single-species biofilm formation on inanimate substrate biological process involved in intraspecies interaction between organisms biological regulation positive regulation of biological process single-species biofilm formation single-species biofilm formation on inanimate substrate positive regulation of single-species biofilm formation aggregation of unicellular organisms submerged biofilm formation regulation of single-species biofilm formation regulation of biological process cell aggregation regulation of cellular process biofilm formation regulation of single-species biofilm formation on inanimate substrate positive regulation of single-species biofilm formation on inanimate substrate biological process involved in intraspecies interaction between organisms biological regulation positive regulation of biological process single-species biofilm formation single-species biofilm formation on inanimate substrate positive regulation of single-species biofilm formation aggregation of unicellular organisms submerged biofilm formation regulation of single-species biofilm formation cellular process single-species submerged biofilm formation positive regulation of cellular process metabolic process regulation of bacterial-type flagellum-dependent cell motility negative regulation of locomotion regulation of cell motility negative regulation of biological process archaeal or bacterial-type flagellum-dependent cell motility cilium or flagellum-dependent cell motility regulation of locomotion negative regulation of cellular process negative regulation of cell motility bacterial-type flagellum-dependent cell motility cell motility negative regulation of bacterial-type flagellum-dependent cell motility locomotion regulation of cellular component organization cell projection organization non-membrane-bounded organelle assembly bacterial-type flagellum assembly negative regulation of organelle assembly cellular component biogenesis cellular component organization cellular component assembly cellular component organization or biogenesis negative regulation of cell projection organization regulation of bacterial-type flagellum assembly organelle assembly negative regulation of cellular component organization regulation of cell projection assembly regulation of cell projection organization regulation of cellular component biogenesis regulation of organelle organization bacterial-type flagellum organization organelle organization negative regulation of organelle organization regulation of organelle assembly cell projection assembly negative regulation of bacterial-type flagellum assembly cell adhesion involved in biofilm formation cell-substrate adhesion cell adhesion involved in single-species biofilm formation cell adhesion	cell pole cellular anatomical entity cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000160	GGDEF domain	Domain
A, B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B	IPR029787	Nucleotide cyclase	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.