4YST
Structure of copper nitrite reductase from Geobacillus thermodenitrificans - 24.9 MGy
Summary for 4YST
| Entry DOI | 10.2210/pdb4yst/pdb |
| Related | 4YSA 4YSC 4YSD 4YSE 4YSO 4YSP 4YSQ 4YSR 4YSS 4YSU |
| Descriptor | Nitrite reductase, COPPER (II) ION, (4S)-2-METHYL-2,4-PENTANEDIOL, ... (5 entities in total) |
| Functional Keywords | nitrite, copper, reductase, oxidoreductase |
| Biological source | Geobacillus thermodenitrificans (strain NG80-2) |
| Total number of polymer chains | 1 |
| Total formula weight | 36118.57 |
| Authors | Fukuda, Y.,Tse, K.M.,Suzuki, M.,Diederichs, K.,Hirata, K.,Nakane, T.,Sugahara, M.,Nango, E.,Tono, K.,Joti, Y.,Kameshima, T.,Song, C.,Hatsui, T.,Yabashi, M.,Nureki, O.,Matsumura, H.,Inoue, T.,Iwata, S.,Mizohata, E. (deposition date: 2015-03-17, release date: 2016-02-24, Last modification date: 2024-03-20) |
| Primary citation | Fukuda, Y.,Tse, K.M.,Suzuki, M.,Diederichs, K.,Hirata, K.,Nakane, T.,Sugahara, M.,Nango, E.,Tono, K.,Joti, Y.,Kameshima, T.,Song, C.,Hatsui, T.,Yabashi, M.,Nureki, O.,Matsumura, H.,Inoue, T.,Iwata, S.,Mizohata, E. Redox-coupled structural changes in nitrite reductase revealed by serial femtosecond and microfocus crystallography J.Biochem., 159:527-538, 2016 Cited by PubMed Abstract: Serial femtosecond crystallography (SFX) has enabled the damage-free structural determination of metalloenzymes and filled the gaps of our knowledge between crystallographic and spectroscopic data. Crystallographers, however, scarcely know whether the rising technique provides truly new structural insights into mechanisms of metalloenzymes partly because of limited resolutions. Copper nitrite reductase (CuNiR), which converts nitrite to nitric oxide in denitrification, has been extensively studied by synchrotron radiation crystallography (SRX). Although catalytic Cu (Type 2 copper (T2Cu)) of CuNiR had been suspected to tolerate X-ray photoreduction, we here showed that T2Cu in the form free of nitrite is reduced and changes its coordination structure in SRX. Moreover, we determined the completely oxidized CuNiR structure at 1.43 Å resolution with SFX. Comparison between the high-resolution SFX and SRX data revealed the subtle structural change of a catalytic His residue by X-ray photoreduction. This finding, which SRX has failed to uncover, provides new insight into the reaction mechanism of CuNiR. PubMed: 26769972DOI: 10.1093/jb/mvv133 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.34 Å) |
Structure validation
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