5YY0

Crystal structure of the HyhL-HypA complex (form II)

Summary for 5YY0

• Entry DOI: 10.2210/pdb5yy0/pdb
• Descriptor: Cytosolic NiFe-hydrogenase, alpha subunit, Probable hydrogenase nickel incorporation protein HypA, ZINC ION (3 entities in total)
• Functional Keywords: hydrogenase, maturation, hyhl, hypa, metal binding protein
• Biological source: Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)); More
• Total number of polymer chains: 2
• Total formula weight: 64129.85

Authors

Kwon, S.,Watanabe, S.,Nishitani, Y.,Miki, K. (deposition date: 2017-12-07, release date: 2018-06-20, Last modification date: 2024-03-27)

Primary citation

Kwon, S.,Watanabe, S.,Nishitani, Y.,Kawashima, T.,Kanai, T.,Atomi, H.,Miki, K.
Crystal structures of a [NiFe] hydrogenase large subunit HyhL in an immature state in complex with a Ni chaperone HypA.
Proc. Natl. Acad. Sci. U.S.A., 115:7045-7050, 2018

PubMed Abstract: Ni-Fe clusters are inserted into the large subunit of [NiFe] hydrogenases by maturation proteins such as the Ni chaperone HypA via an unknown mechanism. We determined crystal structures of an immature large subunit HyhL complexed with HypA from Structure analysis revealed that the N-terminal region of HyhL extends outwards and interacts with the Ni-binding domain of HypA. Intriguingly, the C-terminal extension of immature HyhL, which is cleaved in the mature form, adopts a β-strand adjacent to its N-terminal β-strands. The position of the C-terminal extension corresponds to that of the N-terminal extension of a mature large subunit, preventing the access of endopeptidases to the cleavage site of HyhL. These findings suggest that Ni insertion into the active site induces spatial rearrangement of both the N- and C-terminal tails of HyhL, which function as a key checkpoint for the completion of the Ni-Fe cluster assembly.

PubMed: 29915046
DOI: 10.1073/pnas.1801955115

Experimental method

X-RAY DIFFRACTION (3.243 Å)