4I14

Crystal Structure of Mtb-ribA2 (Rv1415)

Summary for 4I14

• Entry DOI: 10.2210/pdb4i14/pdb
• Related: 3MIO
• Descriptor: Riboflavin biosynthesis protein RibBA, ZINC ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: dhbps, gchii, riba2, gtp, riboflavin, antimicrobial, hydrolase, lyase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 2
• Total formula weight: 92485.48

Authors

Singh, M.,Kumar, P.,Yadav, S.,Gautam, R.,Sharma, N.,Karthikeyan, S. (deposition date: 2012-11-20, release date: 2013-08-28, Last modification date: 2023-11-08)

Primary citation

Singh, M.,Kumar, P.,Yadav, S.,Gautam, R.,Sharma, N.,Karthikeyan, S.
The crystal structure reveals the molecular mechanism of bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II (Rv1415) from Mycobacterium tuberculosis
Acta Crystallogr.,Sect.D, 69:1633-1644, 2013

PubMed Abstract: The enzymes 3,4-dihydroxy-2-butanone 4-phosphate synthase (DHBPS) and GTP cyclohydrolase II (GCHII) catalyze the initial steps of both branches of the bacterial riboflavin-biosynthesis pathway. The structures and molecular mechanisms of DHBPS and GCHII as separate polypeptides are known; however, their organization and molecular mechanism as a bifunctional enzyme are unknown to date. Here, the crystal structure of an essential bifunctional DHBPS/GCHII enzyme from Mycobacterium tuberculosis (Mtb-ribA2) is reported at 3.0 Å resolution. The crystal structure revealed two conformationally different molecules of Mtb-ribA2 in the asymmetric unit that form a dimer via their GCHII domains. Interestingly, analysis of the crystal packing revealed a long `helical-like oligomer' formed by DHBPS and GCHII functional homodimers, thus generating an `open-ended' unit-cell lattice. However, size-exclusion chromatography studies suggest that Mtb-ribA2 exists as a dimer in solution. To understand the discrepancy between the oligomerization observed in solution and in the crystal structure, the DHBPS (Mtb-DHBPS) and GCHII (Mtb-GCHII) domains of Mtb-ribA2 have been cloned, expressed and purified as His-tagged proteins. Size-exclusion chromatography studies indicated that Mtb-GCHII is a dimer while Mtb-DHBPS exists as a monomer in solution. Moreover, kinetic studies revealed that the GCHII activities of Mtb-ribA2 and Mtb-GCHII are similar, while the DHBPS activity of Mtb-ribA2 is much higher than that of Mtb-DHBPS alone. Taken together, the results strongly suggest that Mtb-ribA2 exists as a dimer formed through its GCHII domains and requires full-length Mtb-ribA2 for optimal DHBPS activity.

PubMed: 23999287
DOI: 10.1107/S0907444913011402

Experimental method

X-RAY DIFFRACTION (3 Å)