| Literature DB >> 29581294 |
Xi Zhang1,2,3,4, Qifan Wang1,2,3,4, Jianping Wu1,2,3,4, Jiawei Wang1,2,3,4, Yigong Shi5,2,3,4,6, Minhao Liu5,2,3,4.
Abstract
Lysyl oxidases (LOXs), a type of copper- and lysyl tyrosylquinone (LTQ) -dependent amine oxidase, catalyze the oxidative deamination of lysine residues of extracellular matrix (ECM) proteins such as elastins and collagens and generate aldehyde groups. The oxidative deamination of lysine represents the foundational step for the cross-linking of elastin and collagen and thus is crucial for ECM modeling. Despite their physiological significance, the structure of this important family of enzymes remains elusive. Here we report the crystal structure of human lysyl oxidase-like 2 (hLOXL2) at 2.4-Å resolution. Unexpectedly, the copper-binding site of hLOXL2 is occupied by zinc, which blocks LTQ generation and the enzymatic activity of hLOXL2 in our in vitro assay. Biochemical analysis confirms that copper loading robustly activates hLOXL2 and supports LTQ formation. Furthermore, the LTQ precursor residues in the structure are distanced by 16.6 Å, corroborating the notion that the present structure may represent a precursor state and that pronounced conformational rearrangements would be required for protein activation. The structure presented here establishes an important foundation for understanding the structure-function relationship of LOX proteins and will facilitate LOX-targeting drug discovery.Entities:
Keywords: crystal structure; human LOXL2; lysyl oxidase; precursor state
Mesh:
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Year: 2018 PMID: 29581294 PMCID: PMC5899467 DOI: 10.1073/pnas.1720859115
Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN: 0027-8424 Impact factor: 11.205
Fig. 1.Overall structure of hLOXL2. (A) The reaction and structure of LTQ. (B) Crystal structure of hLOXL2 (residues 318–774, N455Q). The structure is presented in two perpendicular views. The third and fourth SRCR domains are colored cyan and green, respectively; the catalytic domain is colored yellow. The glycosyl groups at Asn644 are shown as black sticks. Zinc and calcium ions are presented as dark blue and green spheres, respectively. All structure figures were prepared using PyMOL (48).
Fig. 2.Structure of the catalytic domain of hLOXL2. (A) Overall structure of the hLOXL2 catalytic domain. The β-sandwich structure that can be superimposed with that of β-galactosidase is defined as the structure core and is colored yellow; the nonoverlapping regions, colored orange, are defined as extra segments (ES1–3). Disulfide bonds are shown as sticks. Bound zinc and calcium are displayed as spheres. (B) Topology of the catalytic domain. The structure core and ES regions are color-coded as in A. The LTQ precursor and the His residues involved in copper binding are indicated.
Fig. 3.The zinc-bound hLOXL2 structure may represent a precursor state. (A) Close-up view of the putative catalytic site of hLOXL2. The LTQ precursors and copper-binding site residues are displayed as sticks; the zinc ion is shown as a sphere. Distances between residues are shown by a dashed line. (B) Element analysis of the crystal-derived hLOXL2. Aliquots of hLOXL2 protein dissolved from crystals were treated with the indicated conditions and subjected to element analysis to determine metal content. Apo, hLOXL2 treated with 1,10-phenanthroline to remove zinc; IC, apo hLOXL2 treated with copper for ion exchange; untreated, the dissolved hLOXL2 proteins without metal chelator treatment. Protein concentrations were calculated based on the sulfur element quantified in the same experiments. (C) Element analysis of the copper-binding site–mutated hLOXL2 variants reveals decreased zinc content. The boundaries of the tested variants are identical to those for crystallization. Control, residues 318–774 with N455Q. (D) Functional assessment of the hLOXL2 samples purified from crystals. The crystal-derived hLOXL2 samples in B were subjected to enzymatic assay. IC+BAPN, 50 μM BAPN was added to the assay to inhibit enzymatic activity. (E) Michaelis–Menten curve and kinetic parameters of ion-exchanged hLOXL2. The initial rates of oxidative deamination were determined using ion-exchanged hLOXL2 (residues 318–774 with N455Q) and were plotted versus a range of DAP (Left) or Lys (Right) concentrations. The Michaelis–Menten curve was fitted, and Km and kcat were calculated. All error bars represent SDs from three independent experiments. Please refer to for details of the enzymatic assays.
Fig. 4.Validation of quinone formation in activated hLOXL2. (A) The UV-Vis scan revealed the characteristic absorption of LTQ in activated hLOXL2 but not in the indicated mutants. hLOXL2 proteins with (Right) or without (Left) phenylhydrazine labeling were subjected to the UV-Vis scan. All samples shown in this figure are based on the construct of residues 318–774 (N455Q) unless otherwise indicated. IC, the indicated variants were treated for ion exchange as in Fig. 3 before analysis. Please refer to for assay details. (B) Mass spectrometric analysis of activated hLOXL2 identified the LTQ-containing peptide. Untreated and ion-exchanged hLOXL2 were labeled with phenylhydrazine and subjected to MS analysis after trypsin digestion. The phenylhydrazine-labeled LTQ-containing peptide was identified only in ion-exchanged hLOXL2 and not in the untreated protein. Cysteine residues modified by carbamidomethyl group are marked with a black star. (Inset) The azo tautomer of phenylhydrazine-labeled LTQ.