Crystal structure of DhbE, an archetype for aryl acid activating domains of modular nonribosomal peptide synthetases

被引:228
作者
May, JJ
Kessler, N
Marahiel, MA
Stubbs, MT
机构
[1] Univ Marburg, Fachbereich Chem, D-35032 Marburg, Germany
[2] Univ Halle Wittenberg, Inst Biotechnol, D-06120 Halle An Der Saale, Germany
关键词
adenylation domain; nonribosomal pepticle synthesis; X-ray crystal structure; antibiotic biosynthesis; siderophore formation;
D O I
10.1073/pnas.182156699
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The synthesis of the catecholic siderophore bacillibactin is accomplished by the nonribosomal peptide synthetase (NRPS) encoded by the dhb operon. DhbE is responsible for the initial step in bacillibactin synthesis, the activation of the aryl acid 2,3-dihydroxy-benzoate (DHB). The stand-alone adenylation (A) domain DhbE, the structure of which is presented here, exhibits greatest homology to other NRPS A-domains, acyl-CoA ligases and luciferases. it's structure is solved in three different states, without the ligands ATP and DHB (native state), with the product DHB-AMP (adenylate state) and with the hydrolyzed product AMP and DHB (hydrolyzed state). The 59.9-kDa protein folds into two domains, with the active site at the interface between them. In contrast to previous proposals of a major reorientation of the large and small domains on substrate binding, we observe only local structural rearrangements. The structure of the phosphate binding loop could be determined, a motif common to many adenylate-forming enzymes, as well as with bound DHB-adenylate and the hydrolyzed product DHB*AMP. Based on the structure and amino acid sequence alignments, an adapted specificity conferring code for aryl acid activating domains is proposed, allowing assignment of substrate specificity to gene products of previously unknown function.
引用
收藏
页码:12120 / 12125
页数:6
相关论文
共 30 条
[1]   Biosynthesis of the ansamycin antibiotic rifamycin: deductions from the molecular analysis of the rif biosynthetic gene cluster of Amycolatopsis mediterranei S699 [J].
August, PR ;
Tang, L ;
Yoon, YJ ;
Ning, S ;
Muller, R ;
Yu, TW ;
Taylor, M ;
Hoffmann, D ;
Kim, CG ;
Zhang, XH ;
Hutchinson, CR ;
Floss, HG .
CHEMISTRY & BIOLOGY, 1998, 5 (02) :69-79
[2]   Firefly luciferase: The structure is known, but the mystery remains [J].
Baldwin, TO .
STRUCTURE, 1996, 4 (03) :223-228
[3]   Crystallography & NMR system:: A new software suite for macromolecular structure determination [J].
Brunger, AT ;
Adams, PD ;
Clore, GM ;
DeLano, WL ;
Gros, P ;
Grosse-Kunstleve, RW ;
Jiang, JS ;
Kuszewski, J ;
Nilges, M ;
Pannu, NS ;
Read, RJ ;
Rice, LM ;
Simonson, T ;
Warren, GL .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 :905-921
[4]   Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S [J].
Conti, E ;
Stachelhaus, T ;
Marahiel, MA ;
Brick, P .
EMBO JOURNAL, 1997, 16 (14) :4174-4183
[5]   Crystal structure of firefly luciferase throws light on a superfamily of adenylate-forming enzymes [J].
Conti, E ;
Franks, NP ;
Brick, P .
STRUCTURE, 1996, 4 (03) :287-298
[6]   Active site of lysyl-tRNA synthetase: Structural studies of the adenylation reaction [J].
Desogus, G ;
Todone, F ;
Brick, P ;
Onesti, S .
BIOCHEMISTRY, 2000, 39 (29) :8418-8425
[7]   Structural basis for the inhibition of firefly luciferase by a general anesthetic [J].
Franks, NP ;
Jenkins, A ;
Conti, E ;
Lieb, WR ;
Brick, P .
BIOPHYSICAL JOURNAL, 1998, 75 (05) :2205-2211
[8]   ANALYSIS OF CORE SEQUENCES IN THE D-PHE ACTIVATING DOMAIN OF THE MULTIFUNCTIONAL PEPTIDE SYNTHETASE TYCA BY SITE-DIRECTED MUTAGENESIS [J].
GOCHT, M ;
MARAHIEL, MA .
JOURNAL OF BACTERIOLOGY, 1994, 176 (09) :2654-2662
[9]  
Harwood C. R., 1990, MOL BIOL METHODS BAC
[10]   SELENOMETHIONYL PROTEINS PRODUCED FOR ANALYSIS BY MULTIWAVELENGTH ANOMALOUS DIFFRACTION (MAD) - A VEHICLE FOR DIRECT DETERMINATION OF 3-DIMENSIONAL STRUCTURE [J].
HENDRICKSON, WA ;
HORTON, JR ;
LEMASTER, DM .
EMBO JOURNAL, 1990, 9 (05) :1665-1672