Database accession: MF7000975
Name: Domain-swapped guanine deaminase (Bacillus subtilis)
PDB ID: 1wkq
Experimental method: X-ray (1.17 Å)
Assembly: Homodimer
Source organism: Bacillus subtilis
Primary publication of the structure:
Liaw SH, Chang YJ, Lai CT, Chang HC, Chang GG
Crystal structure of Bacillus subtilis guanine deaminase: the first domain-swapped structure in the cytidine deaminase superfamily.
(2004) J. Biol. Chem. 279: 35479-85
PMID: 15180998
Abstract:
Guanine deaminase, a key enzyme in the nucleotide metabolism, catalyzes the hydrolytic deamination of guanine into xanthine. The crystal structure of the 156-residue guanine deaminase from Bacillus subtilis has been solved at 1.17-A resolution. Unexpectedly, the C-terminal segment is swapped to form an intersubunit active site and an intertwined dimer with an extensive interface of 3900 A(2) per monomer. The essential zinc ion is ligated by a water molecule together with His(53), Cys(83), and Cys(86). A transition state analog was modeled into the active site cavity based on the tightly bound imidazole and water molecules, allowing identification of the conserved deamination mechanism and specific substrate recognition by Asp(114) and Tyr(156'). The closed conformation also reveals that substrate binding seals the active site entrance, which is controlled by the C-terminal tail. Therefore, the domain swapping has not only facilitated the dimerization but has also ensured specific substrate recognition. Finally, a detailed structural comparison of the cytidine deaminase superfamily illustrates the functional versatility of the divergent active sites found in the guanine, cytosine, and cytidine deaminases and suggests putative specific substrate-interacting residues for other members such as dCMP deaminases.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
guanine deaminase activity guanine deaminase activity
guanosine deaminase activity guanosine deaminase activity
zinc ion binding zinc ion binding
Biological process:
guanine catabolic process guanine catabolic process
purine nucleoside catabolic process purine nucleoside catabolic process
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Guanine deaminase
Source organism: Bacillus subtilis
Length: 156 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNHETFLKRAVTLACEGVNAGIGGPFGAVIVKDGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQLDDCILYTSCEPCPMCLGAIYWARPKAVFYAAEHTDAAEAGFDDSFIYKEIDKPAEERTIPFYQVTLTEHLSPFQAWRNFANKKEY
UniProtKB AC: O34598 (positions: 1-156)
Coverage: 100%
Name: Guanine deaminase
Source organism: Bacillus subtilis
Length: 156 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNHETFLKRAVTLACEGVNAGIGGPFGAVIVKDGAIIAEGQNNVTTSNDPTAHAEVTAIRKACKVLGAYQLDDCILYTSCEPCPMCLGAIYWARPKAVFYAAEHTDAAEAGFDDSFIYKEIDKPAEERTIPFYQVTLTEHLSPFQAWRNFANKKEY
UniProtKB AC: O34598 (positions: 2-156)
Coverage: 99%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: -
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Analytical ultracentrifugation experiments demonstrated that the guanine deaminase enzyme exists in solution as a homodimer. The C-terminal segment is swapped to form an intersubunit active site and an intertwined dimer with an extensive interface. The dimer is stabilized mainly by the formation of the wide interhelical hydrophobic packing of helices. Interestingly, analysis of unswapped bGD model shows that domain swapping contributes not only to oligomerization and structural stability but also to substrate specificity (PMID:15180998).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). No related structure was found in the MFIB database.
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