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PDBsum entry 2vva

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Lyase PDB id
2vva
Jmol
Contents
Protein chain
258 a.a.
Ligands
SO4
CO2 ×2
GOL ×2
Metals
_ZN
Waters ×350

References listed in PDB file
Key reference
Title Structural study of X-Ray induced activation of carbonic anhydrase.
Authors B.Sjoblom, M.Polentarutti, K.Djinovic-Carugo.
Ref. Proc.Natl.Acad.Sci.USA, 2009, 106, 10609-10613. [DOI no: 10.1073/pnas.0904184106]
PubMed id 19520834
Abstract
Carbonic anhydrase, a zinc metalloenzyme, catalyzes the reversible hydration of carbon dioxide to bicarbonate. It is involved in processes connected with acid-base homeostasis, respiration, and photosynthesis. More than 100 distinct human carbonic anhydrase II (HCAII) 3D structures have been generated in last 3 decades [Liljas A, et al. (1972) Nat New Biol 235:131-137], but a structure of an HCAII in complex with CO(2) or HCO(3)(-) has remained elusive. Here, we report previously undescribed structures of HCAII:CO(2) and HCAII:HCO(3)(-) complexes, together with a 3D molecular film of the enzymatic reaction observed successively in the same crystal after extended exposure to X-ray. We demonstrate that the unexpected enzyme activation was caused in an X-ray dose-dependent manner. Although X-ray damage to macromolecular samples has long been recognized [Ravelli RB, Garman EF (2006) Curr Opin Struct Biol 16:624-629], the detailed structural analysis reports on X-ray-driven reactions have been very rare in literature to date. Here, we report on enzyme activation and the associated chemical reaction in a crystal at 100 K. We propose mechanisms based on water photoradiolysis and/or electron radiolysis as the main cause of enzyme activation.
Figure 2.
Stereoview of HCAII in complex with carbon dioxide and bicarbonate. Distances listed below are indicated in the figures by dashed lines. (A) The 1σ level 2|F[o]| − |F[c]| electron density map and corresponding model for the CO[2]-loaded HCAII active site at 1.56-Å resolution. The carbon dioxide O2 atom is at a hydrogen-bonding distance of 3.4 Å from the main chain nitrogen of Thr-199, Wat-338 (3.1 Å), and Wat-263 (3.1 Å). The CO[2] molecule also makes van der Waals contacts with all residues lining the hydrophobic pocket (Val-121, Val-143, Leu-198, and Trp-209) and the zinc ligands His-94 and His-119. (B) The 1σ level 2|Fo| – |Fc| electron density maps and the corresponding model for the complex of HCAII and bicarbonate at 1.66-Å resolution. The O3 oxygen of bicarbonate is bound to the zinc ion at 2.0 Å and is within hydrogen-bonding distance of Wat-318 (2.4 Å), Thr-199 OG1 (2.6 Å), and Wat-338 (2.9 Å). The bicarbonate O2 atom is within hydrogen-bonding distance of Wat-338 (2.7 Å) and Thr-199 N (3.1 Å). The O1 atom of bicarbonate is 2.9 Å away from the zinc ion. The HCO[3]^− has van der Waals contacts with the same residues as CO[2] (see A).
Figure 3.
Stereoview of the overlay of the resting enzyme with the substrate and product. Superposition of active sites of resting enzyme (red), enzyme with CO[2] substrate (green), and enzyme with bound HCO[3]^− (yellow). Arrows indicate potential pathways of the water molecules from the entrance of the active-site channel toward the catalytic site.
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