2Z1U

Crystal Structure of Hydrogenase Maturation Protein HypE in complex with ATP

Summary for 2Z1U

• Entry DOI: 10.2210/pdb2z1u/pdb
• Related: 2Z1T
• Descriptor: Hydrogenase expression/formation protein HypE, MAGNESIUM ION, ADENOSINE-5'-TRIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: alpha-beta fold, beta barrel, lyase
• Biological source: Desulfovibrio vulgaris subsp. vulgaris
• Total number of polymer chains: 1
• Total formula weight: 36651.98

Authors

Shomura, Y.,Higuchi, Y. (deposition date: 2007-05-15, release date: 2007-10-09, Last modification date: 2024-03-13)

Primary citation

Shomura, Y.,Komori, H.,Miyabe, N.,Tomiyama, M.,Shibata, N.,Higuchi, Y.
Crystal Structures of Hydrogenase Maturation Protein HypE in the Apo and ATP-bound Forms
J.Mol.Biol., 372:1045-1054, 2007

PubMed Abstract: The hydrogenase maturation protein HypE serves an essential function in the biosynthesis of the nitrile group, which is subsequently coordinated to Fe as CN(-) ligands in [Ni-Fe] hydrogenase. Here, we present the crystal structures of HypE from Desulfovibrio vulgaris Hildenborough in the presence and in the absence of ATP at a resolution of 2.0 A and 2.6 A, respectively. Comparison of the apo structure with the ATP-bound structure reveals that binding ATP causes an induced-fit movement of the N-terminal portion, but does not entail an overall structural change. The residue Cys341 at the C terminus, whose thiol group is supposed to be carbamoylated before the nitrile group synthesis, is completely buried within the protein and is located in the vicinity of the gamma-phosphate group of the bound ATP. This suggests that the catalytic reaction occurs in this configuration but that a conformational change is required for the carbamoylation of Cys341. A glutamate residue is found close to the thiol group as well, which is suggestive of deprotonation of the carbamoyl group at the beginning of the reactions.

PubMed: 17706667
DOI: 10.1016/j.jmb.2007.07.023

Experimental method

X-RAY DIFFRACTION (2 Å)