General Information

Database accession: MF7000480

Name: Ni-bound GloA2

PDB ID: 4mtq PDBe

Experimental method: X-ray (2.17 Å)

Assembly: Homodimer

Source organism: Pseudomonas aeruginosa

Primary publication of the structure:

Bythell-Douglas R, Suttisansanee U, Flematti GR, Challenor M, Lee M, Panjikar S, Honek JF, Bond CS
The crystal structure of a homodimeric Pseudomonas glyoxalase I enzyme reveals asymmetric metallation commensurate with half-of-sites activity.

(2015) Chemistry 21: 541-4

PMID: 25411134 PubMed

Abstract:

The Zn inactive class of glyoxalase I (Glo1) metalloenzymes are typically homodimeric with two metal-dependent active sites. While the two active sites share identical amino acid composition, this class of enzyme is optimally active with only one metal per homodimer. We have determined the X-ray crystal structure of GloA2, a Zn inactive Glo1 enzyme from Pseudomonas aeruginosa. The presented structures exhibit an unprecedented metal-binding arrangement consistent with half-of-sites activity: one active site contains a single activating Ni(2+) ion, whereas the other contains two inactivating Zn(2+) ions. Enzymological experiments prompted by the binuclear Zn(2+) site identified a novel catalytic property of GloA2. The enzyme can function as a Zn(2+) /Co(2+) -dependent hydrolase, in addition to its previously determined glyoxalase I activity. The presented findings demonstrate that GloA2 can accommodate two distinct metal-binding arrangements simultaneously, each of which catalyzes a different reaction.


Function and Biology Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown.

Molecular function:

lactoylglutathione lyase activity lactoylglutathione lyase activity GeneOntology

metal ion binding metal ion binding GeneOntology

Biological process:

methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione GeneOntology

Cellular component:

cytoplasm cytoplasm GeneOntology

Structure Summary 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


Chain A

Name: Aldoketomutase

Source organism: Pseudomonas aeruginosa

Length: 131 residues

Sequence:Sequence according to the corresponding UniProt protein segmentMRILHSMLRVADLEAALEFYTRALDMRLLRRRDYPEGRFTLAFVGYQDERAAAALELTHNWDRDGYTQGDGYGHLAIEVEDAAVTCARARALGYRVTREAGLMQHGRSVIAFLEDPDGYKVELIQKGTQFD

UniProtKB AC: Q9I5L8 (positions: 1-128) UniProt

Coverage: 97%

Chain B

Name: Aldoketomutase

Source organism: Pseudomonas aeruginosa

Length: 131 residues

Sequence:Sequence according to the corresponding UniProt protein segmentMRILHSMLRVADLEAALEFYTRALDMRLLRRRDYPEGRFTLAFVGYQDERAAAALELTHNWDRDGYTQGDGYGHLAIEVEDAAVTCARARALGYRVTREAGLMQHGRSVIAFLEDPDGYKVELIQKGTQFD

UniProtKB AC: Q9I5L8 (positions: 1-128) UniProt

Coverage: 97%

Evidence Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding.

Representative domain in related structures: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily

Evidence level: Indirect evidence

Evidence coverage: The full structure participates in mutual synergistic folding.

Complex Evidence:

The VOC superfamily of metalloenzymes is characterized by a three-dimensional domain-swapped arrangement of tandem βαβββ-motifs (PMID:24447055). The original gene duplication event led to the βαβββ tandem structure, which appears to require dimerization for stability. Two different forms of domain-swapped dimers may coexist in solution (PMID:12121648) in which both subunits of the homodimer participate in coordination of each metal ion and formation of the U-shaped active sites in the enzyme (PMID:24004181). The complex is predominantly dimeric in solution (gel filtration) (PMID:12121648).

Chain A:

N/A

Chain B:

N/A

Surface and contacts features:

Related Structure(s) 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).

There are 64 related structures in the MFIB database:
The molecule viewer shows our modified stucture.

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