3WJR

crystal structure of HypE in complex with a nucleotide

Summary for 3WJR

• Entry DOI: 10.2210/pdb3wjr/pdb
• Related: 2Z1E 2Z1F 3WJP 3WJQ
• Descriptor: Hydrogenase expression/formation protein HypE, BENZAMIDINE, ADENOSINE MONOPHOSPHATE, ... (9 entities in total)
• Functional Keywords: [nife]hydrogenase maturation, lyase
• Biological source: Thermococcus kodakarensis
• Total number of polymer chains: 1
• Total formula weight: 37394.96

Authors

Tominaga, T.,Watanabe, S.,Miki, K. (deposition date: 2013-10-14, release date: 2013-12-18, Last modification date: 2023-11-08)

Primary citation

Tominaga, T.,Watanabe, S.,Matsumi, R.,Atomi, H.,Imanaka, T.,Miki, K.
Crystal structures of the carbamoylated and cyanated forms of HypE for [NiFe] hydrogenase maturation
Proc.Natl.Acad.Sci.USA, 110:20485-20490, 2013

PubMed Abstract: Hydrogenase pleiotropically acting protein (Hyp)E plays a role in biosynthesis of the cyano groups for the NiFe(CN)2CO center of [NiFe] hydrogenases by catalyzing the ATP-dependent dehydration of the carbamoylated C-terminal cysteine of HypE to thiocyanate. Although structures of HypE proteins have been determined, until now there has been no structural evidence to explain how HypE dehydrates thiocarboxamide into thiocyanate. Here, we report the crystal structures of the carbamoylated and cyanated forms of HypE from Thermococcus kodakarensis in complex with nucleotides at 1.53- and 1.64-Å resolution, respectively. Carbamoylation of the C-terminal cysteine (Cys338) of HypE by chemical modification is clearly observed in the present structures. In the presence of ATP, the thiocarboxamide of Cys338 is successfully dehydrated into the thiocyanate. In the carbamoylated state, the thiocarboxamide nitrogen atom of Cys338 is close to a conserved glutamate residue (Glu272), but the spatial position of Glu272 is less favorable for proton abstraction. On the other hand, the thiocarboxamide oxygen atom of Cys338 interacts with a conserved lysine residue (Lys134) through a water molecule. The close contact of Lys134 with an arginine residue lowers the pKa of Lys134, suggesting that Lys134 functions as a proton acceptor. These observations suggest that the dehydration of thiocarboxamide into thiocyanate is catalyzed by a two-step deprotonation process, in which Lys134 and Glu272 function as the first and second bases, respectively.

PubMed: 24297906
DOI: 10.1073/pnas.1313620110

Experimental method

X-RAY DIFFRACTION (1.864 Å)