1V3W

Structure of Ferripyochelin binding protein from Pyrococcus horikoshii OT3

Summary for 1V3W

• Entry DOI: 10.2210/pdb1v3w/pdb
• Descriptor: ferripyochelin binding protein, ZINC ION, CALCIUM ION, ... (7 entities in total)
• Functional Keywords: beta-helix, carbonic anhydrase, structural genomics, riken structural genomics/proteomics initiative, rsgi, transferase
• Biological source: Pyrococcus horikoshii
• Total number of polymer chains: 1
• Total formula weight: 19484.15

Authors

Jeyakanthan, J.,Tahirov, T.H.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2003-11-07, release date: 2003-11-18, Last modification date: 2023-10-25)

Primary citation

Jeyakanthan, J.,Rangarajan, S.,Mridula, P.,Kanaujia, S.P.,Shiro, Y.,Kuramitsu, S.,Yokoyama, S.,Sekar, K.
Observation of a calcium-binding site in the gamma-class carbonic anhydrase from Pyrococcus horikoshii.
Acta Crystallogr.,Sect.D, 64:1012-1019, 2008

PubMed Abstract: Carbonic anhydrases are zinc-containing metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. Three crystal structures of gamma-class carbonic anhydrase (one of which is bound to a bicarbonate molecule) from the aerobic OT3 strain of the hyperthermophilic archeon Pyrococcus horikoshii have been solved by molecular replacement in space group F4(1)32. The asymmetric unit contains a monomer of 173 amino acids and a catalytic Zn2+ ion. The protein fold is a regular prism formed by a left-handed beta-helix, similar to previously reported structures. The active-site Zn2+ ion located at the interface between the two monomers is bound to three histidyl residues and a water molecule in a tetrahedral fashion. In addition to the 20 beta-strands comprising the beta-helix, there is also a long C-terminal alpha-helix. For the first time, Ca2+ ions have been observed in addition to the catalytic Zn2+ ion. It is hypothesized that Tyr159 (which corresponds to the catalytically important Asn202 in previously reported structures) utilizes C-H...pi interactions to fulfill its functions. This study may shed light on the catalytic mechanism of the enzyme and throw open new questions on the mechanism of product removal in carbonic anhydrases.

PubMed: 18931408
DOI: 10.1107/S0907444908024323

Experimental method

X-RAY DIFFRACTION (1.5 Å)