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High-resolution solution structure of the catalytic fragment of human collagenase-3 (MMP-13) complexed with a hydroxamic acid inhibitor.

Moy FJ, Chanda PK, Chen JM, Cosmi S, Edris W, Levin JI, Powers R
J Mol Biol 302 671-89 (2000)
Cited: 28 times
EuropePMC logo PMID: 10986126

Abstract

The high-resolution solution structure of the catalytic fragment of human collagenase-3 (MMP-13) complexed with a sulfonamide derivative of a hydroxamic acid compound (WAY-151693) has been determined by multidimensional heteronuclear NMR. A total of 30 structures were calculated for residues 7-164 by means of hybrid distance geometry-simulated annealing using a total of 3280 experimental NMR restraints. The atomic rms distribution about the mean coordinate positions for the 30 structures is 0.43(+/-0.05) A for the backbone atoms, 0.80(+/-0.09) A for all atoms, and 0.47(+/-0.04) A for all atoms excluding disordered side-chains. The overall structure of MMP-13 is composed of a beta-sheet consisting of five beta-strands in a mixed parallel and anti-parallel arrangement and three alpha-helices where its overall fold is consistent with previously solved MMP structures. A comparison of the NMR structure of MMP-13 with the published 1.6 A resolution X-ray structure indicates that the major differences between the structures is associated with loop dynamics and crystal-packing interactions. The side-chains of some active-site residues for the NMR and X-ray structures of MMP-13 adopt distinct conformations. This is attributed to the presence of unique inhibitors in the two structures that encounter distinct interactions with MMP-13. The major structural difference observed between the MMP-13 and MMP-1 NMR structures is the relative size and shape of the S1' pocket where this pocket is significantly longer for MMP-13, nearly reaching the surface of the protein. Additionally, MMP-1 and MMP-13 exhibit different dynamic properties for the active-site loop and the structural Zn-binding region. The inhibitor WAY-151693 is well defined in the MMP-13 active-site based on a total of 52 distance restraints. The binding motif of WAY-151693 in the MMP-13 complex is consistent with our previously reported MMP-1:CGS-27023A NMR structure and is similar to the MMP-13: RS-130830 X-ray structure.

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  14. Matrix metalloproteinase-inhibitor interaction: the solution structure of the catalytic domain of human matrix metalloproteinase-3 with different inhibitors. Alcaraz LA, Banci L, Bertini I, Cantini F, Donaire A, Gonnelli L. J Biol Inorg Chem 12 1197-1206 (2007)
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  16. Apparent tradeoff of higher activity in MMP-12 for enhanced stability and flexibility in MMP-3. Liang X, Arunima A, Zhao Y, Bhaskaran R, Shende A, Byrne TS, Fleeks J, Palmier MO, Van Doren SR. Biophys J 99 273-283 (2010)
  17. An insight to conserved water molecular dynamics of catalytic and structural Zn(+2) ions in matrix metalloproteinase 13 of human. Chakrabarti B, Bairagya HR, Mallik P, Mukhopadhyay BP, Bera A. J Biomol Struct Dyn 28 503-516 (2011)
  18. Calcium regulates tertiary structure and enzymatic activity of human endometase/matrilysin-2 and its role in promoting human breast cancer cell invasion. Lee S, Park HI, Sang QX. Biochem J 403 31-42 (2007)
  19. Crystal structures of the catalytic domain of human stromelysin-1 (MMP-3) and collagenase-3 (MMP-13) with a hydroxamic acid inhibitor SM-25453. Kohno T, Hochigai H, Yamashita E, Tsukihara T, Kanaoka M. Biochem Biophys Res Commun 344 315-322 (2006)
  20. Pyrone-based inhibitors of metalloproteinase types 2 and 3 may work as conformation-selective inhibitors. Durrant JD, de Oliveira CA, McCammon JA. Chem Biol Drug Des 78 191-198 (2011)
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  23. The Developmental Transcription Factor p63 Is Redeployed to Drive Allergic Skin Inflammation through Phosphorylation by p38α. Jiménez-Andrade Y, Hillette KR, Yoshida T, Kashiwagi M, Choo MK, Liang Y, Georgopoulos K, Park JM. J Immunol 208 2613-2621 (2022)


Related citations provided by authors (1)

  1. Letter to the editor: 1H, 15N, 13C, and 13CO assignments and secondary structure determination of collagenase-3 (MMP-13) complexed with a hydroxamic acid inhibitor.. Moy FJ, Chanda PK, Cosmi S, Edris W, Levin JI, Powers R J Biomol NMR 17 269-70 (2000)

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