6LV5

Ni- Carbonic Anhydrase II pH 7.8 0 atm CO2

Summary for 6LV5

• Entry DOI: 10.2210/pdb6lv5/pdb
• Related: 6LUU
• Descriptor: Carbonic anhydrase 2, GLYCEROL, NICKEL (II) ION, ... (4 entities in total)
• Functional Keywords: metalloenzymes; carbonic anhydrase; enzyme mechanism; metal coordination geometry; proton transfer; biological water dynamics, metal binding protein-lyase complex, metal binding protein/lyase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 29498.54

Authors

Kim, C.U.,Kim, J.K. (deposition date: 2020-02-02, release date: 2020-08-19, Last modification date: 2023-11-29)

Primary citation

Kim, J.K.,Lee, C.,Lim, S.W.,Adhikari, A.,Andring, J.T.,McKenna, R.,Ghim, C.M.,Kim, C.U.
Elucidating the role of metal ions in carbonic anhydrase catalysis.
Nat Commun, 11:4557-4557, 2020

PubMed Abstract: Why metalloenzymes often show dramatic changes in their catalytic activity when subjected to chemically similar but non-native metal substitutions is a long-standing puzzle. Here, we report on the catalytic roles of metal ions in a model metalloenzyme system, human carbonic anhydrase II (CA II). Through a comparative study on the intermediate states of the zinc-bound native CA II and non-native metal-substituted CA IIs, we demonstrate that the characteristic metal ion coordination geometries (tetrahedral for Zn, tetrahedral to octahedral conversion for Co, octahedral for Ni, and trigonal bipyramidal for Cu) directly modulate the catalytic efficacy. In addition, we reveal that the metal ions have a long-range (~10 Å) electrostatic effect on restructuring water network in the active site. Our study provides evidence that the metal ions in metalloenzymes have a crucial impact on the catalytic mechanism beyond their primary chemical properties.

PubMed: 32917908
DOI: 10.1038/s41467-020-18425-5

Experimental method

X-RAY DIFFRACTION (1.2 Å)