1k2x
From Proteopedia
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{{Structure | {{Structure | ||
|PDB= 1k2x |SIZE=350|CAPTION= <scene name='initialview01'>1k2x</scene>, resolution 1.65Å | |PDB= 1k2x |SIZE=350|CAPTION= <scene name='initialview01'>1k2x</scene>, resolution 1.65Å | ||
| - | |SITE= | + | |SITE= <scene name='pdbsite=AC1:Na+Binding+Site+For+Residue+A+801'>AC1</scene>, <scene name='pdbsite=AC2:Na+Binding+Site+For+Residue+C+802'>AC2</scene>, <scene name='pdbsite=AC3:Cl+Binding+Site+For+Residue+A+803'>AC3</scene>, <scene name='pdbsite=AC4:Cl+Binding+Site+For+Residue+C+804'>AC4</scene>, <scene name='pdbsite=AC5:Cl+Binding+Site+For+Residue+D+805'>AC5</scene>, <scene name='pdbsite=AC6:Cl+Binding+Site+For+Residue+D+806'>AC6</scene>, <scene name='pdbsite=AC7:Cl+Binding+Site+For+Residue+C+807'>AC7</scene>, <scene name='pdbsite=AC8:Cl+Binding+Site+For+Residue+A+808'>AC8</scene>, <scene name='pdbsite=AC9:Cl+Binding+Site+For+Residue+C+809'>AC9</scene>, <scene name='pdbsite=BC1:Cl+Binding+Site+For+Residue+A+810'>BC1</scene> and <scene name='pdbsite=BC2:Cl+Binding+Site+For+Residue+A+811'>BC2</scene> |
|LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> | |LIGAND= <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=CME:S,S-(2-HYDROXYETHYL)THIOCYSTEINE'>CME</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> | ||
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </span> | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Asparaginase Asparaginase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.1.1 3.5.1.1] </span> | ||
|GENE= ybiK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | |GENE= ybiK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli]) | ||
| - | |DOMAIN= | + | |DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd04701 Asparaginase_2]</span> |
|RELATEDENTRY=[[1jn9|1JN9]], [[1apz|1APZ]], [[1ayy|1AYY]], [[2gac|2GAC]], [[2gaw|2GAW]], [[9gaa|9GAA]], [[9gac|9GAC]], [[9gaf|9GAF]], [[1apy|1APY]] | |RELATEDENTRY=[[1jn9|1JN9]], [[1apz|1APZ]], [[1ayy|1AYY]], [[2gac|2GAC]], [[2gaw|2GAW]], [[9gaa|9GAA]], [[9gac|9GAC]], [[9gaf|9GAF]], [[1apy|1APY]] | ||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k2x OCA], [http://www.ebi.ac.uk/pdbsum/1k2x PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1k2x RCSB]</span> | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1k2x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1k2x OCA], [http://www.ebi.ac.uk/pdbsum/1k2x PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1k2x RCSB]</span> | ||
}} | }} | ||
| - | ''' | + | '''Crystal structure of putative asparaginase encoded by Escherichia coli ybiK gene''' |
| + | |||
| + | ==Overview== | ||
| + | Plant-type L-asparaginases hydrolyze the side-chain amide bond of L-asparagine or its beta-peptides. They belong to the N-terminal nucleophile (Ntn) hydrolases and are synthesized as inactive precursor molecules. Activation occurs via the autoproteolytic release of two subunits, alpha and beta, the latter of which carries the nucleophile at its N-terminus. Crystallographic studies of plant-type asparaginases have focused on an Escherichia coli homologue (EcAIII), which has been crystallized in several crystal forms. Although they all belong to the same P2(1)2(1)2(1) space group with similar unit-cell parameters, they display different crystal-packing arrangements and thus should be classified as separate polymorphs. This variability stems mainly from different positions of the EcAIII molecules within the unit cell, although they also exhibit slight differences in orientation. The intermolecular interactions that trigger different crystal lattice formation are mediated by ions, which represent the most variable component of the crystallization conditions. This behaviour confirms recent observations that small molecules might promote protein crystal lattice formation. | ||
==About this Structure== | ==About this Structure== | ||
1K2X is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K2X OCA]. | 1K2X is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K2X OCA]. | ||
| + | |||
| + | ==Reference== | ||
| + | Crystal packing of plant-type L-asparaginase from Escherichia coli., Michalska K, Borek D, Hernandez-Santoyo A, Jaskolski M, Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):309-20. Epub 2008, Feb 20. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18323626 18323626] | ||
[[Category: Asparaginase]] | [[Category: Asparaginase]] | ||
[[Category: Escherichia coli]] | [[Category: Escherichia coli]] | ||
| Line 26: | Line 32: | ||
[[Category: ntn hydrolase]] | [[Category: ntn hydrolase]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 2 11:31:27 2008'' |
Revision as of 08:31, 2 April 2008
| |||||||
| , resolution 1.65Å | |||||||
|---|---|---|---|---|---|---|---|
| Sites: | , , , , , , , , , and | ||||||
| Ligands: | , , | ||||||
| Gene: | ybiK (Escherichia coli) | ||||||
| Activity: | Asparaginase, with EC number 3.5.1.1 | ||||||
| Domains: | Asparaginase_2 | ||||||
| Related: | 1JN9, 1APZ, 1AYY, 2GAC, 2GAW, 9GAA, 9GAC, 9GAF, 1APY
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of putative asparaginase encoded by Escherichia coli ybiK gene
Overview
Plant-type L-asparaginases hydrolyze the side-chain amide bond of L-asparagine or its beta-peptides. They belong to the N-terminal nucleophile (Ntn) hydrolases and are synthesized as inactive precursor molecules. Activation occurs via the autoproteolytic release of two subunits, alpha and beta, the latter of which carries the nucleophile at its N-terminus. Crystallographic studies of plant-type asparaginases have focused on an Escherichia coli homologue (EcAIII), which has been crystallized in several crystal forms. Although they all belong to the same P2(1)2(1)2(1) space group with similar unit-cell parameters, they display different crystal-packing arrangements and thus should be classified as separate polymorphs. This variability stems mainly from different positions of the EcAIII molecules within the unit cell, although they also exhibit slight differences in orientation. The intermolecular interactions that trigger different crystal lattice formation are mediated by ions, which represent the most variable component of the crystallization conditions. This behaviour confirms recent observations that small molecules might promote protein crystal lattice formation.
About this Structure
1K2X is a Protein complex structure of sequences from Escherichia coli. Full crystallographic information is available from OCA.
Reference
Crystal packing of plant-type L-asparaginase from Escherichia coli., Michalska K, Borek D, Hernandez-Santoyo A, Jaskolski M, Acta Crystallogr D Biol Crystallogr. 2008 Mar;64(Pt 3):309-20. Epub 2008, Feb 20. PMID:18323626
Page seeded by OCA on Wed Apr 2 11:31:27 2008
