6PWJ | pdb_00006pwj

Vibrio cholerae LapD S helix-GGDEF-EAL (apo)

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	GGDEF	e6pwjB2	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	EAL	e6pwjB1	A: a/b barrels	X: TIM beta/alpha-barrel	H: EAL domain (From Topology)	T: EAL domain	F: EAL	ECOD (1.6)
A	GGDEF	e6pwjA2	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	EAL	e6pwjA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: EAL domain (From Topology)	T: EAL domain	F: EAL	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
B	3.20.20.450	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	EAL domain	CATH (utative)
A	3.30.70.270	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Reverse transcriptase/Diguanylate cyclase domain	CATH (utative)
A	3.20.20.450	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	EAL domain	CATH (utative)

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
A, B	PF00563	EAL domain (EAL)	EAL domain	This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function [1]. The domain contains many conserved acidic residues that ...	This domain is found in diverse bacterial signaling proteins. It is called EAL after its conserved residues. The EAL domain is a good candidate for a diguanylate phosphodiesterase function [1]. The domain contains many conserved acidic residues that could participate in metal binding and might form the phosphodiesterase active site [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	GGDEF and EAL domain-containing protein	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds phosphoric diester hydrolase activity cyclic-guanylate-specific phosphodiesterase activity hydrolase activity catalytic activity cation binding ion binding metal ion binding	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation cellular process signal transduction cell communication	cellular anatomical structure membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR000160	GGDEF domain	Domain
A, B	IPR003660	HAMP domain	Domain
A, B	IPR032244	LapD/MoxY, periplasmic domain	Domain
A, B	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B	IPR050706	Cyclic di-GMP phosphodiesterase-like	Family
A, B	IPR042461	LapD/MoxY periplasmic domain, C-terminal	Homologous Superfamily
A, B	IPR001633	EAL domain	Domain
A, B	IPR035919	EAL domain superfamily	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.