Annotations: 1W25

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d1w25b1	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Response regulator PleD, receiver domain	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
B	d1w25b3	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleotide cyclase	GGDEF domain	Response regulator PleD, C-terminal domain	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
B	d1w25b4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
A	d1w25a1	Alpha and beta proteins (a/b)	Flavodoxin-like	CheY-like	CheY-related	Response regulator PleD, receiver domain	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
A	d1w25a3	Alpha and beta proteins (a+b)	Ferredoxin-like	Nucleotide cyclase	GGDEF domain	Response regulator PleD, C-terminal domain	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)
A	d1w25a4	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Caulobacter vibrioides CB15 ) [TaxId: 190650 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8043226	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CheY-like	8043222	3001156	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CheY-like	8043224	3001156	SCOP2B (2022-06-29)
A	SCOP2 Family	CheY-related	8030843	4003632	SCOP2 (2022-06-29)
A	SCOP2 Family	CheY-related	8030845	4003632	SCOP2 (2022-06-29)
A	SCOP2 Family	GGDEF domain	8030847	4003808	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CheY-like	8043222	3001156	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	CheY-like	8043224	3001156	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8043226	3001272	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)
B	GGDEF	e1w25B1	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	Response_reg	e1w25B2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Response_reg	ECOD (1.6)
A	GGDEF	e1w25A1	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)
A	Response_reg	e1w25A2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: Response_reg	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	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)
A	3.40.50.2300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Response regulator	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00072	Response regulator receiver domain (Response_reg)	Response regulator receiver domain	This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.	Domain
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	STALKED-CELL DIFFERENTIATION CONTROLLING PROTEIN	transferase activity nucleotidyltransferase activity catalytic activity diguanylate cyclase activity transferase activity, transferring phosphorus-containing groups binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding transferase activity nucleotidyltransferase activity catalytic activity diguanylate cyclase activity transferase activity, transferring phosphorus-containing groups binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding cation binding metal ion binding	developmental process cellular developmental process cell differentiation cellular process cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication signal transduction developmental process cellular developmental process cell differentiation cellular process cellular response to stimulus regulation of biological process phosphorelay signal transduction system regulation of cellular process response to stimulus signaling biological regulation intracellular signal transduction cell communication signal transduction 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 cell adhesion involved in biofilm formation cell aggregation biofilm formation biological process involved in intraspecies interaction between organisms cell-substrate adhesion single-species biofilm formation aggregation of unicellular organisms submerged biofilm formation cell adhesion involved in single-species biofilm formation cell adhesion single-species submerged biofilm formation	cell periphery cellular anatomical structure plasma membrane membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011006	CheY-like superfamily	Homologous Superfamily
A, B	IPR050469	Bacterial Diguanylate Cyclase	Family
A, B	IPR000160	GGDEF domain	Domain
A, B	IPR001789	Signal transduction response regulator, receiver 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 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.