7LKJ

Crystal structure of Helicobacter pylori aminofutalosine deaminase (AFLDA)

Summary for 7LKJ

• Entry DOI: 10.2210/pdb7lkj/pdb
• Descriptor: Aminofutalosine deaminase, FE (III) ION, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: aminofutalosine deaminase, aflda, inhibitor, inhibitor complex, h. pylori, hydrolase
• Biological source: Helicobacter pylori
• Total number of polymer chains: 4
• Total formula weight: 190558.41

Authors

Harijan, R.K.,Feng, M.,Bonanno, J.B.,Almo, S.C.,Schramm, V.L. (deposition date: 2021-02-02, release date: 2021-06-23, Last modification date: 2023-10-18)

Primary citation

Feng, M.,Harijan, R.K.,Harris, L.D.,Tyler, P.C.,Frohlich, R.F.G.,Brown, M.,Schramm, V.L.
Aminofutalosine Deaminase in the Menaquinone Pathway of Helicobacter pylori .
Biochemistry, 60:1933-1946, 2021

PubMed Abstract: is a Gram-negative bacterium that is responsible for gastric and duodenal ulcers. uses the unusual pathway with aminofutalosine (AFL) as an intermediate for menaquinone biosynthesis. Previous reports indicate that hydrolysis of AFL by 5'-methylthioadenosine nucleosidase (MTAN) is the direct path for producing downstream metabolites in the pathway. However, genomic analysis indicates is a candidate for encoding AFL deaminase (AFLDA), an activity for deaminating aminofutolasine. The product, futalosine, is not a known substrate for bacterial MTANs. Recombinant jhp0252 was expressed and characterized as an AFL deaminase (AFLDA). Its catalytic specificity includes AFL, 5'-methylthioadenosine, 5'-deoxyadenosine, adenosine, and -adenosylhomocysteine. The / value for AFL is 6.8 × 10 M s, 26-fold greater than that for adenosine. 5'-Methylthiocoformycin (MTCF) is a slow-onset inhibitor for AFLDA and demonstrated inhibitory effects on growth. Supplementation with futalosine partially restored growth under MTCF treatment, suggesting AFL deamination is significant for cell growth. The crystal structures of apo-AFLDA and with MTCF at the catalytic sites show a catalytic site Zn or Fe as the water-activating group. With bound MTCF, the metal ion is 2.0 Å from the sp hydroxyl group of the transition state analogue. Metabolomics analysis revealed that AFLDA has intracellular activity and is inhibited by MTCF. The pathway in bifurcates at aminofutalosine with MTAN producing adenine and depurinated futalosine and AFLDA producing futalosine. Inhibition of cellular MTAN or AFLDA decreased the cellular content of menaquinone-6, supporting roles for both enzymes in the pathway.

PubMed: 34077175
DOI: 10.1021/acs.biochem.1c00215

Experimental method

X-RAY DIFFRACTION (2.79 Å)