This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.




1dih

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /><applet load="1dih" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dih, resolution 2.2&Aring;" /> '''THREE-DIMENSIONAL STR...)
Current revision (06:54, 7 February 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1dih.gif|left|200px]]<br /><applet load="1dih" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1dih, resolution 2.2&Aring;" />
 
-
'''THREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REDUCTASE'''<br />
 
-
==Overview==
+
==THREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REDUCTASE==
-
Dihydrodipicolinate reductase is an enzyme found in bacteria and higher, plants involved in the biosynthesis of diaminopimelic acid and lysine., Because these pathways are unique to bacteria and plants, they may, represent attractive targets for new antimicrobial or herbicidal, compounds. The three-dimensional structure of Escherichia coli, dihydrodipicolinate reductase, complexed with NADPH, has been determined, and refined to a crystallographic R-factor of 18.6% with diffraction data, to 2.2 A resolution. The refined model contains the complete protein, chain, the cofactor NADPH, and 55 water molecules. The enzyme is composed, of two domains. The dinucleotide binding domain has a central, seven-stranded parallel beta-sheet surrounded by four alpha-helices, with, the cofactor binding site located at the carboxy-terminal edge of the, sheet. The second domain contains four beta-strands and two alpha-helices, that form an open mixed beta-sandwich. A possible binding site for, dihydrodipicolinate has been identified in this second domain, about 12 A, away from the dinucleotide binding site. This would imply that the protein, must undergo some conformational change in order to perform catalysis. In, the crystal, the native enzyme is a homotetramer generated by a 222, crystallographic axis. Implications of the tetrameric structure for the, enzyme function are presented. Dihydrodipicolinate reductase uses both, NADH and NADPH as cofactors, and analysis of its cofactor binding site, allows for a molecular understanding of the enzyme's dual specificity.
+
<StructureSection load='1dih' size='340' side='right'caption='[[1dih]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1dih]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DIH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DIH FirstGlance]. <br>
-
1DIH is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with NDP as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Dihydrodipicolinate_reductase Dihydrodipicolinate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.1.26 1.3.1.26] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DIH OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-
 
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
-
==Reference==
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dih FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dih OCA], [https://pdbe.org/1dih PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dih RCSB], [https://www.ebi.ac.uk/pdbsum/1dih PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dih ProSAT]</span></td></tr>
-
Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase., Scapin G, Blanchard JS, Sacchettini JC, Biochemistry. 1995 Mar 21;34(11):3502-12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7893645 7893645]
+
</table>
-
[[Category: Dihydrodipicolinate reductase]]
+
== Function ==
 +
[https://www.uniprot.org/uniprot/DAPB_ECOLI DAPB_ECOLI] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate. Can use both NADH and NADPH as a reductant, with NADH being twice as effective as NADPH.<ref>PMID:7893644</ref> <ref>PMID:20503968</ref>
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/di/1dih_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=1dih ConSurf].
 +
<div style="clear:both"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Blanchard, J.S.]]
+
[[Category: Blanchard JS]]
-
[[Category: Sacchettini, J.C.]]
+
[[Category: Sacchettini JC]]
-
[[Category: Scapin, G.]]
+
[[Category: Scapin G]]
-
[[Category: NDP]]
+
-
[[Category: oxidoreductase]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:18:09 2007''
+

Current revision

THREE-DIMENSIONAL STRUCTURE OF E. COLI DIHYDRODIPICOLINATE REDUCTASE

PDB ID 1dih

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dih"
Personal tools