Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus

Abstract

The crystal structure of a conserved hypothetical protein, Aq1575, from Aquifex aeolicus has been determined by using x-ray crystallography. The protein belongs to the domain of unknown function DUF28 in the Pfam and PALI databases for which there was no structural information available until now. A structural homology search with the DALI algorithm indicates that this protein has a new fold with no obvious similarity to those of other proteins of known three-dimensional structure. The protein reveals a monomer consisting of three domains arranged along a pseudo threefold symmetry axis. There is a large cleft with approximate dimensions of 10 Å ؋ 10 Å ؋ 20 Å in the center of the three domains along the symmetry axis. Two possible active sites are suggested based on the structure and multiple sequence alignment. There are several highly conserved residues in these putative active sites. The structure based molecular properties and thermostability of the protein are discussed.structural genomics ͉ new fold ͉ DUF28 ͉ hyperthermophile ͉ thermostability

NMR structure of the conserved hypothetical protein TM0979 from Thermotoga maritima

“…13 FFAS showed that the hypothetical protein ychN 14 (PDBid: 1JX7) from E. coli was the closest structural neighbor, which is in excellent agreement with the aforementioned analysis. DALI identified the hypothetical protein MTH1491 15 (PDBid: 1L1S) from Methanobacterium thermoautotrophicum as the closest structural neighbor.…”

Novel Genes of the dsr Gene Cluster and Evidence for Close Interaction of Dsr Proteins during Sulfur Oxidation in the Phototrophic Sulfur Bacterium Allochromatium vinosum

“…DsrE belongs to the Cluster of Orthologous Group COG1553 (National Center for Biotechnology Information database, National Library of Medicine, National Institutes of Health), for which structural information is available. The crystal structure of YchN from E. coli, a protein of unknown function, has been described (67). It shows a dimer of homotrimers arranged in a cylindrical ring structure.…”

The YebC Family Protein PA0964 Negatively Regulates thePseudomonas aeruginosaQuinolone Signal System and Pyocyanin Production

“…However, this group of proteins has been characterized from a structural perspective. The X-ray structures of YebC proteins from Aquifex aeolicus (45), E. coli, and Helicobacter pylori have been solved (Protein Data Bank entries 1lfp, 1kon, and 1mw7, respectively). Structural analysis revealed a large cavity with a predominance of negatively charged residues on the surface of this protein (45).…”

“…The X-ray structures of YebC proteins from Aquifex aeolicus (45), E. coli, and Helicobacter pylori have been solved (Protein Data Bank entries 1lfp, 1kon, and 1mw7, respectively). Structural analysis revealed a large cavity with a predominance of negatively charged residues on the surface of this protein (45). Intriguingly, all three crystal structure solved proteins have a putative DNA binding function and a domain sharing topological similarity with the Tet repressor class D variant (Protein Data Bank [http://www.rcsb.org/pdb]).…”