1q11
From Proteopedia
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|PDB= 1q11 |SIZE=350|CAPTION= <scene name='initialview01'>1q11</scene>, resolution 1.6Å | |PDB= 1q11 |SIZE=350|CAPTION= <scene name='initialview01'>1q11</scene>, resolution 1.6Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TYB:TYROSINAL'>TYB</scene> |
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Tyrosine--tRNA_ligase Tyrosine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.1 6.1.1.1] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1n3l|1N3L]], [[1ntg|1NTG]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1q11 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q11 OCA], [http://www.ebi.ac.uk/pdbsum/1q11 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1q11 RCSB]</span> | ||
}} | }} | ||
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==Overview== | ==Overview== | ||
Early forms of the genetic code likely generated "statistical" proteins, with similar side chains occupying the same sequence positions at different ratios. In this scenario, groups of related side chains were treated by aminoacyl-tRNA synthetases as a single molecular species until a discrimination mechanism developed that could separate them. The aromatic amino acids tryptophan, tyrosine, and phenylalanine likely constituted one of these groups. A crystal structure of human tryptophanyl-tRNA synthetase was solved at 2.1 A with a tryptophanyl-adenylate bound at the active site. A cocrystal structure of an active fragment of human tyrosyl-tRNA synthetase with its cognate amino acid analog was also solved at 1.6 A. The two structures enabled active site identifications and provided the information for structure-based sequence alignments of approximately 45 orthologs of each enzyme. Two critical positions shared by all tyrosyl-tRNA synthetases and tryptophanyl-tRNA synthetases for amino acid discrimination were identified. The variations at these two positions and phylogenetic analyses based on the structural information suggest that, in contrast to many other amino acids, discrimination of tyrosine from tryptophan occurred late in the development of the genetic code. | Early forms of the genetic code likely generated "statistical" proteins, with similar side chains occupying the same sequence positions at different ratios. In this scenario, groups of related side chains were treated by aminoacyl-tRNA synthetases as a single molecular species until a discrimination mechanism developed that could separate them. The aromatic amino acids tryptophan, tyrosine, and phenylalanine likely constituted one of these groups. A crystal structure of human tryptophanyl-tRNA synthetase was solved at 2.1 A with a tryptophanyl-adenylate bound at the active site. A cocrystal structure of an active fragment of human tyrosyl-tRNA synthetase with its cognate amino acid analog was also solved at 1.6 A. The two structures enabled active site identifications and provided the information for structure-based sequence alignments of approximately 45 orthologs of each enzyme. Two critical positions shared by all tyrosyl-tRNA synthetases and tryptophanyl-tRNA synthetases for amino acid discrimination were identified. The variations at these two positions and phylogenetic analyses based on the structural information suggest that, in contrast to many other amino acids, discrimination of tyrosine from tryptophan occurred late in the development of the genetic code. | ||
| - | |||
| - | ==Disease== | ||
| - | Known disease associated with this structure: Charcot-Marie-Tooth disease, dominant intermediate C OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=603623 603623]] | ||
==About this Structure== | ==About this Structure== | ||
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[[Category: Schimmel, P.]] | [[Category: Schimmel, P.]] | ||
[[Category: Yang, X L.]] | [[Category: Yang, X L.]] | ||
| - | [[Category: GOL]] | ||
| - | [[Category: K]] | ||
| - | [[Category: PO4]] | ||
| - | [[Category: TYB]] | ||
[[Category: anticodon recognition domain]] | [[Category: anticodon recognition domain]] | ||
[[Category: rossmann fold domain containing the active site]] | [[Category: rossmann fold domain containing the active site]] | ||
[[Category: substrate analog tyrosinol co-crystalized]] | [[Category: substrate analog tyrosinol co-crystalized]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:07:20 2008'' |
Revision as of 20:07, 30 March 2008
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| , resolution 1.6Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Activity: | Tyrosine--tRNA ligase, with EC number 6.1.1.1 | ||||||
| Related: | 1N3L, 1NTG
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of an active fragment of human tyrosyl-tRNA synthetase with tyrosinol
Overview
Early forms of the genetic code likely generated "statistical" proteins, with similar side chains occupying the same sequence positions at different ratios. In this scenario, groups of related side chains were treated by aminoacyl-tRNA synthetases as a single molecular species until a discrimination mechanism developed that could separate them. The aromatic amino acids tryptophan, tyrosine, and phenylalanine likely constituted one of these groups. A crystal structure of human tryptophanyl-tRNA synthetase was solved at 2.1 A with a tryptophanyl-adenylate bound at the active site. A cocrystal structure of an active fragment of human tyrosyl-tRNA synthetase with its cognate amino acid analog was also solved at 1.6 A. The two structures enabled active site identifications and provided the information for structure-based sequence alignments of approximately 45 orthologs of each enzyme. Two critical positions shared by all tyrosyl-tRNA synthetases and tryptophanyl-tRNA synthetases for amino acid discrimination were identified. The variations at these two positions and phylogenetic analyses based on the structural information suggest that, in contrast to many other amino acids, discrimination of tyrosine from tryptophan occurred late in the development of the genetic code.
About this Structure
1Q11 is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.
Reference
Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains., Yang XL, Otero FJ, Skene RJ, McRee DE, Schimmel P, Ribas de Pouplana L, Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15376-80. Epub 2003 Dec 11. PMID:14671330
Page seeded by OCA on Sun Mar 30 23:07:20 2008
