Crystal structures of hydrogenase maturation protein HypE in the Apo and ATP-bound forms.
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.
Shomura
Yasuhito
Y
Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan. Electronic address: shomura@sci.u-hyogo.ac.jp.
Komori
Hirofumi
H
Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan.
Miyabe
Natsuko
N
Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan.
Tomiyama
Masamitsu
M
National Institute of Agrobiological Sciences, 2-1-2 Konnondai, Tsukuba, Ibaraki 305-8602, Japan.
Shibata
Naoki
N
Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan.
Higuchi
Yoshiki
Y
Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori-cho, Ako-gun, Hyogo 678-1297, Japan; RIKEN SPring-8 Center, 1-1-1 Koto, Sayo-gun, Sayo-cho, Hyogo 679-5148, Japan. Electronic address: hig@sci.u-hyogo.ac.jp.
D000255:Adenosine Triphosphate / Q000737:chemistry / Q000378:metabolism*; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D018360:Crystallography, X-Ray; D016969:Desulfovibrio vulgaris / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009570:Nitriles / Q000737:chemistry; D017434:Protein Structure, Tertiary; D011687:Purines / Q000096:biosynthesis / Q000737:chemistry; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
D001426:Bacterial Proteins; D009570:Nitriles; D011687:Purines; C085871:hypE protein, Bacteria; D000255:Adenosine Triphosphate