Structural characterization of the enzymes composing the arginine deiminase pathway in Mycoplasma penetrans.
Structural characterization of the enzymes composing the arginine deiminase pathway in Mycoplasma penetrans.
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DOI：
10.1371/journal.pone.0047886
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Reverter D
中科院分区：
文献类型：
--
作者：
Gallego P;Planell R;Benach J;Querol E;Perez-Pons JA;Reverter D
精氨酸向ATP合成的代谢被认为是微生物如厌氧条件下的反式支原体的主要能量来源。此外，该途径还涉及某些微生物的致病和毒力机制，即在感染期间保护免受酸性胁迫。在这项工作中，我们提出的晶体结构的三个酶组成的基因簇的精氨酸脱亚胺酶途径从M。反式精氨酸脱亚胺酶（ADI）、鸟氨酸氨甲酰转移酶（OTC）和氨基甲酸激酶（CK）。精氨酸脱亚胺酶（ADI）的结构已被细化到2.3 μ m的分辨率在其apo形式，显示了“开放”构象的酶的活性位点相比，以前的复杂结构与底物中间体。ADI的活性位点口袋是空的，其中一些催化和结合残基远离其活性位置，表明底物结合后的主要构象变化。鸟氨酸氨甲酰基转移酶（OTC）已被精制成两种晶体形式，分别在2.5 μ m和2.6 μ m分辨率下，均显示具有23点对称性的相同十二聚体结构。OTC的十二聚体结构代表了该蛋白质家族中的最高水平的组织，并且在M. pastrans中，它由四个催化同源三聚体之间的新界面构成。氨基甲酸激酶（CK）的结构特征是在活性部位存在两个硫酸根离子，一个在氨基甲酰磷酸结合部位，另一个在酶的β-磷酸ADP结合口袋。CK结构还显示了调节酶催化活性的一些元素的变化。代谢途径的数量相对较少以及与人类致病性相关的反式支原体将精氨酸脱亚胺酶途径酶作为设计针对该人类寄生虫的特异性抑制剂的潜在靶标。
The metabolism of arginine towards ATP synthesis has been considered a major source of energy for microorganisms such as Mycoplasma penetrans in anaerobic conditions. Additionally, this pathway has also been implicated in pathogenic and virulence mechanism of certain microorganisms, i.e. protection from acidic stress during infection. In this work we present the crystal structures of the three enzymes composing the gene cluster of the arginine deiminase pathway from M. penetrans: arginine deiminase (ADI), ornithine carbamoyltransferase (OTC) and carbamate kinase (CK). The arginine deiminase (ADI) structure has been refined to 2.3 Å resolution in its apo-form, displaying an “open” conformation of the active site of the enzyme in comparison to previous complex structures with substrate intermediates. The active site pocket of ADI is empty, with some of the catalytic and binding residues far from their active positions, suggesting major conformational changes upon substrate binding. Ornithine carbamoyltransferase (OTC) has been refined in two crystal forms at 2.5 Å and 2.6 Å resolution, respectively, both displaying an identical dodecameric structure with a 23-point symmetry. The dodecameric structure of OTC represents the highest level of organization in this protein family and in M.penetrans it is constituted by a novel interface between the four catalytic homotrimers. Carbamate kinase (CK) has been refined to 2.5 Å resolution and its structure is characterized by the presence of two ion sulfates in the active site, one in the carbamoyl phosphate binding site and the other in the β-phosphate ADP binding pocket of the enzyme. The CK structure also shows variations in some of the elements that regulate the catalytic activity of the enzyme. The relatively low number of metabolic pathways and the relevance in human pathogenesis of Mycoplasma penetrans places the arginine deiminase pathway enzymes as potential targets to design specific inhibitors against this human parasite.
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DOI：
10.1107/s0907444909052925
发表时间：
2010-02
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
Adams PD;Afonine PV;Bunkóczi G;Chen VB;Davis IW;Echols N;Headd JJ;Hung LW;Kapral GJ;Grosse-Kunstleve RW;McCoy AJ;Moriarty NW;Oeffner R;Read RJ;Richardson DC;Richardson JS;Terwilliger TC;Zwart PH
通讯作者：
Zwart PH
影响因子：
11.4
作者：
Humm, A;Fritsche, E;Huber, R
通讯作者：
Huber, R
影响因子：
4.8
作者：
Knodler, LA;Sekyere, EO;Edwards, MR
通讯作者：
Edwards, MR
DOI：
10.1073/pnas.81.15.4864
发表时间：
1984-01-01
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA-BIOLOGICAL SCIENCES
影响因子：
--
作者：
HOUGHTON, JE;BENCINI, DA;WILD, JR
通讯作者：
WILD, JR
影响因子：
5.6
作者：
HONZATKO, RB;CRAWFORD, JL;LIPSCOMB, WN
通讯作者：
LIPSCOMB, WN