2B0J
The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)
Summary for 2B0J
| Entry DOI | 10.2210/pdb2b0j/pdb |
| Descriptor | 5,10-methenyltetrahydromethanopterin hydrogenase (2 entities in total) |
| Functional Keywords | rossmann fold, helix bundle, oxidoreductase |
| Biological source | Methanocaldococcus jannaschii |
| Total number of polymer chains | 1 |
| Total formula weight | 38739.07 |
| Authors | Pilak, O.,Mamat, B.,Vogt, S.,Hagemeier, C.H.,Thauer, R.K.,Shima, S.,Vonrhein, C.,Warkentin, E.,Ermler, U. (deposition date: 2005-09-14, release date: 2006-04-18, Last modification date: 2024-04-03) |
| Primary citation | Pilak, O.,Mamat, B.,Vogt, S.,Hagemeier, C.H.,Thauer, R.K.,Shima, S.,Vonrhein, C.,Warkentin, E.,Ermler, U. The Crystal Structure of the Apoenzyme of the Iron-Sulphur Cluster-free Hydrogenase J.Mol.Biol., 358:798-809, 2006 Cited by PubMed Abstract: The iron-sulphur cluster-free hydrogenase (Hmd, EC 1.12.98.2) from methanogenic archaea is a novel type of hydrogenase that tightly binds an iron-containing cofactor. The iron is coordinated by two CO molecules, one sulphur and a pyridone derivative, which is linked via a phosphodiester bond to a guanosine base. We report here on the crystal structure of the Hmd apoenzyme from Methanocaldococcus jannaschii at 1.75 A and from Methanopyrus kandleri at 2.4 A resolution. Homodimeric Hmd reveals a unique architecture composed of one central and two identical peripheral globular units. The central unit is composed of the intertwined C-terminal segments of both subunits, forming a novel intersubunit fold. The two peripheral units consist of the N-terminal domain of each subunit. The Rossmann fold-like structure of the N-terminal domain contains a mononucleotide-binding site, which could harbour the GMP moiety of the cofactor. Another binding site for the iron-containing cofactor is most probably Cys176, which is located at the bottom of a deep intersubunit cleft and which has been shown to be essential for enzyme activity. Adjacent to the iron of the cofactor modelled as a ligand to Cys176, an extended U-shaped extra electron density, interpreted as a polyethyleneglycol fragment, suggests a binding site for the substrate methenyltetrahydromethanopterin. PubMed: 16540118DOI: 10.1016/j.jmb.2006.02.035 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.75 Å) |
Structure validation
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