5XGD | pdb_00005xgd

Crystal structure of the PAS-GGDEF-EAL domain of PA0861 from Pseudomonas aeruginosa in complex with GTP


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AGGDEFe5xgdA3 A: a+b two layersX: Alpha-beta plaitsH: Adenylyl and guanylyl cyclase catalytic domain-likeT: Adenylyl and guanylyl cyclase catalytic domain-likeF: GGDEFECOD (1.6)
APASe5xgdA1 A: a+b three layersX: Profilin-likeH: sensor domains (From Topology)T: sensor domainsF: PASECOD (1.6)
AEALe5xgdA2 A: a/b barrelsX: TIM beta/alpha-barrelH: EAL domain (From Topology)T: EAL domainF: EALECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.30.450.20 Alpha Beta 2-Layer Sandwich Beta-Lactamase PAS domainCATH (utative)
A3.30.70.270 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Reverse transcriptase/Diguanylate cyclase domainCATH (utative)
A3.20.20.450 Alpha Beta Alpha-Beta Barrel TIM Barrel EAL domainCATH (utative)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF00989PAS fold (PAS)PAS foldThe PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ [5 ...The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs [4]. The PAS fold appears in archaea, eubacteria and eukarya. This domain can bind gases (O2, CO and NO), FAD, 4-hydroxycinnamic acid and NAD+ [5].
Domain
PF00990Diguanylate cyclase, GGDEF domain (GGDEF)Diguanylate cyclase, GGDEF domainThis 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
PF00563EAL domain (EAL)EAL domainThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Uncharacterized protein PA0861