Crystal structure of aspartate racemase from Pyrococcus horikoshii OT3 and its implications for molecular mechanism of PLP-independent racemization

Journal of Molecular Biology

Volumn 319, Issue 2, 2002, Pages 479-489

  Liu, Lijun ^a   Iwata, Kousuke ^b   Kita, Akiko ^a   Kawarabayasi, Yutaka ^c   Yohda, Masafumi ^b   Miki, Kunio ^a,d  

^a KYOTO UNIVERSITY   (Japan)

^b TOKYO UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (Japan)

^c NATIONAL INSTITUTE OF TECHNOLOGY AND EVALUATION   (Japan)

^d RIKEN Harima Institute/SPring 8 ^*  (Japan)

Author keywords

Aspartate racemase; Molecular recognition; PLP independent racemase; Pyrococcus horikoshii OT3; Structural symmetry

Indexed keywords

ACID; ASPARTATE RACEMASE; BASE; CYSTEINE; DIMER;

ARCHAEBACTERIUM; ARTICLE; BACTERIAL STRAIN; BETA SHEET; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENANTIOMER; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME MECHANISM; ENZYME STABILITY; ENZYME STRUCTURE; ENZYME SUBUNIT; HYPOTHESIS; MOLECULAR MECHANICS; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PYROCOCCUS; R FACTOR; X RAY CRYSTALLOGRAPHY;

ARCHAEA; PYROCOCCUS; PYROCOCCUS HORIKOSHII;

EID: 0036301494     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(02)00296-6     Document Type: Article

References (49)

1. Enzymes in the D-alanine branch of bacterial cell wall peptidoglycan assembly
2. Gene for aspartate racemase from the sulfur-dependent hyperthermophilic archaeum, Desulfurococcus strain SY
3. Occurrence of free D-amino acids and aspartate racemases in hyperthermophilic archaea
4. The presence of free D-aspartic acid in rodents and man
5. Endogenous D-serine in rat brain: N-methyl-D-aspartate receptor-related distribution and aging
6. Human serine racemase: Molecular cloning, genomic organization and functional analysis
7. D-Aspartate disposition in neuronal and endocrine tissues: Ontogeny, biosynthesis and release
8. Studies on amino acid racemases. I. Partial purification and properties of the alanine racemase from Lactobacillus fermenti
9. Mandelate racemase and class-related enzymes
10. Pyridoxal enzymes acting on D-amino acids
11. Cloning and expression in Escherichia coli of the glutamate racemase gene from Pediococcus pentosaceus
12. Energetics and mechanism of proline racemase
13. Expression of recombinant diaminopimelate epimerase in Escherichia coli. Isolation and inhibition with an irreversible inhibitor
14. Kinetic and structural studies of hydroxyproline 2-epimerase
15. Mechanism of the reaction catalyzed by glutamate racemase
16. Isotope effects and the identification of the catalytic residues in the reaction catalyzed by glutamate racemase
17. Chemical mechanism of Haemophilus influenzae diaminopimelate epimerase
18. Energetics of proline racemase: Transition-state fractionation factors for the two protons involved in the catalytic steps
19. Properties of aspartate racemase, a pyridoxal 5′-phosphate-independent amino acid racemase
20. Structure and mechanism of glutamate racemase from Aquifex pyrophilus
21. Structural symmetry: The three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase
22. Bacterial glutamate racemase has high sequence similarity with myoglobins and forms an equimolar inactive complex with hemin
23. Database of homology-derived protein structures and the structural meaning of sequence alignment
24. Multiple sequence alignment with hierarchical clustering
25. Distribution and purification of aspartate racemase in lactic acid bacteria
26. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect
27. Molecular mechanism for dimerization to regulate the catalytic activity of human cytomegalovirus protease
28. How do thermophilic proteins deal with heat?
29. Hydrogen bonds and proton transfer in general-catalytic transition-state stabilization in enzyme catalysis
30. Hydrogen bonds involving sulfur atoms in proteins
31. Structural mechanisms for domain movements in proteins
32. Hard and soft acids and bases
33. More hydrogen bonds for the (structural) biologist
34. UDP-N-acetylmuramyl-L-alanine functions as an activator in the regulation of the Escherichia coli glutamate racemase
35. Catalytic acid/base residues of glutamate racemase
36. Determination of the structure of alanine racemase from Bacillus stearothermophilus at 1.9 Å resolution
37. Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5 Å resolution: Identification of the active site and possible catalytic residues
38. Crystal structure of 7,8-dihydroneopterin triphosphate epimerase
39. Human UDP-galactose 4-epimerase
40. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
41. Crystallization and preliminary X-ray analysis of aspartate racemase from Pyrococcus horikoshii OT3
42. AMoRe: An automated package for molecular replacement
43. Molecular data processing
44. Processing of X-ray diffraction data collected in oscillation mode
45. The CCP4 suite: Programs for protein crystallography
46. Improved methods for building protein models in electron density maps and location of errors in these models
47. Crystallography and NMR system: A new software suite for macromolecular structure determination
48. MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
49. Raster3D: Photo-realistic molecular graphics