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[[Image:1kgt.gif|left|200px]]


{{Structure
==Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA==
|PDB= 1kgt |SIZE=350|CAPTION= <scene name='initialview01'>1kgt</scene>, resolution 2.3&Aring;
<StructureSection load='1kgt' size='340' side='right'caption='[[1kgt]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
|SITE=
== Structural highlights ==
|LIGAND= <scene name='pdbligand=PML:PIMELIC+ACID'>PML</scene>, <scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene>
<table><tr><td colspan='2'>[[1kgt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_variant_bovis Mycobacterium tuberculosis variant bovis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KGT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KGT FirstGlance]. <br>
|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/2,3,4,5-tetrahydropyridine-2,6-dicarboxylate_N-succinyltransferase 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.117 2.3.1.117] </span>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
|GENE= dapD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1765 Mycobacterium bovis])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PML:PIMELIC+ACID'>PML</scene>, <scene name='pdbligand=SCA:SUCCINYL-COENZYME+A'>SCA</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1kgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kgt OCA], [https://pdbe.org/1kgt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1kgt RCSB], [https://www.ebi.ac.uk/pdbsum/1kgt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1kgt ProSAT]</span></td></tr>
|RELATEDENTRY=[[1tdt|1TDT]], [[2tdt|2TDT]], [[3tdt|3TDT]], [[1kgq|1KGQ]]
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1kgt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kgt OCA], [http://www.ebi.ac.uk/pdbsum/1kgt PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kgt RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/DAPD_UNKP DAPD_UNKP]
 
== Evolutionary Conservation ==
'''Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA'''
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
 
  <jmolCheckbox>
==Overview==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/kg/1kgt_consurf.spt"</scriptWhenChecked>
Tetrahydrodipicolinate N-succinyltransferase (DapD) catalyzes the succinyl-CoA-dependent acylation of L-2-amino-6-oxopimelate to 2-N-succinyl-6-oxopimelate as part of the succinylase branch of the meso-diaminopimelate/lysine biosynthetic pathway of bacteria, blue-green algae, and plants. This pathway provides meso-diaminopimelate as a building block for cell wall peptidoglycan in most bacteria, and is regarded as a target pathway for antibacterial agents. We have solved the X-ray crystal structures of DapD in ternary complexes with pimelate/succinyl-CoA and L-2-aminopimelate with the nonreactive cofactor analog, succinamide-CoA. These structures define the binding conformation of the cofactor succinyl group and its interactions with the enzyme and place its thioester carbonyl carbon in close proximity to the nucleophilic 2-amino group of the acceptor, in support of a direct attack ternary complex mechanism. The acyl group specificity differences between homologous tetrahydrodipicolinate N-acetyl- and N-succinyltransferases can be rationalized with reference to at least three amino acids that interact with or give accessible active site volume to the cofactor succinyl group. These residues account at least in part for the substrate specificity that commits metabolic intermediates to either the succinylase or acetylase branches of the meso-diaminopimelate/lysine biosynthetic pathway.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
1KGT is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_bovis Mycobacterium bovis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KGT OCA].  
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1kgt ConSurf].
 
<div style="clear:both"></div>
==Reference==
__TOC__
Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase., Beaman TW, Vogel KW, Drueckhammer DG, Blanchard JS, Roderick SL, Protein Sci. 2002 Apr;11(4):974-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11910040 11910040]
</StructureSection>
[[Category: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase]]
[[Category: Large Structures]]
[[Category: Mycobacterium bovis]]
[[Category: Mycobacterium tuberculosis variant bovis]]
[[Category: Single protein]]
[[Category: Beaman TW]]
[[Category: Beaman, T W.]]
[[Category: Blanchard JS]]
[[Category: Blanchard, J S.]]
[[Category: Drueckhammer DG]]
[[Category: Drueckhammer, D G.]]
[[Category: Roderick SL]]
[[Category: Roderick, S L.]]
[[Category: Vogel KW]]
[[Category: Vogel, K W.]]
[[Category: left-handed parallel beta helix]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:48:24 2008''

Latest revision as of 10:24, 14 February 2024

Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoACrystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with Pimelate and Succinyl-CoA

Structural highlights

1kgt is a 1 chain structure with sequence from Mycobacterium tuberculosis variant bovis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DAPD_UNKP

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

1kgt, resolution 2.30Å

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