1c3v: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(16 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1c3v.gif|left|200px]]


{{Structure
==DIHYDRODIPICOLINATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND PDC==
|PDB= 1c3v |SIZE=350|CAPTION= <scene name='initialview01'>1c3v</scene>, resolution 2.39&Aring;
<StructureSection load='1c3v' size='340' side='right'caption='[[1c3v]], [[Resolution|resolution]] 2.39&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene> and <scene name='pdbligand=PG4:TETRAETHYLENE GLYCOL'>PG4</scene>
<table><tr><td colspan='2'>[[1c3v]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C3V FirstGlance]. <br>
|ACTIVITY= [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]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.39&#8491;</td></tr>
|GENE=
<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>, <scene name='pdbligand=PDC:PYRIDINE-2,6-DICARBOXYLIC+ACID'>PDC</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene></td></tr>
}}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1c3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c3v OCA], [https://pdbe.org/1c3v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c3v RCSB], [https://www.ebi.ac.uk/pdbsum/1c3v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c3v ProSAT]</span></td></tr>
 
</table>
'''DIHYDRODIPICOLINATE REDUCTASE FROM MYCOBACTERIUM TUBERCULOSIS COMPLEXED WITH NADPH AND PDC'''
== Function ==
 
[https://www.uniprot.org/uniprot/DAPB_MYCTU DAPB_MYCTU] Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate (Probable). Can use both NADH and NADPH as a reductant, with NADH being 6-fold as effective as NADPH.<ref>PMID:12962488</ref>
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
Dihydrodipicolinate reductase (DHPR) catalyzes the reduced pyridine nucleotide-dependent reduction of the alpha,beta-unsaturated cyclic imine, dihydrodipicolinate, to generate tetrahydrodipicolinate. This enzyme catalyzes the second step in the bacterial biosynthetic pathway that generates meso-diaminopimelate, a component of bacterial cell walls, and the amino acid L-lysine. The Mycobacterium tuberculosis dapB-encoded DHPR has been cloned, expressed, purified, and crystallized in two ternary complexes with NADH or NADPH and the inhibitor 2,6-pyridinedicarboxylate (2,6-PDC). The structures have been solved using molecular replacement strategies, and the DHPR-NADH-2,6-PDC and DHPR-NADPH-2,6-PDC complexes have been refined against data to 2.3 and 2.5 A, respectively. The M. tuberculosis DHPR is a tetramer of identical subunits, with each subunit composed of two domains connected by two flexible hinge regions. The N-terminal domain binds pyridine nucleotide, while the C-terminal domain is involved in both tetramer formation and substrate/inhibitor binding. The M. tuberculosis DHPR uses NADH and NADPH with nearly equal efficiency based on V/K values. To probe the nature of this substrate specificity, we have generated two mutants, K9A and K11A, residues that are close to the 2'-phosphate of NADPH. These two mutants exhibit decreased specificity for NADPH by factors of 6- and 30-fold, respectively, but the K11A mutant exhibits 270% of WT activity using NADH. The highly conserved structure of the nucleotide fold may permit other enzyme's nucleotide specificity to be altered using similar mutagenic strategies.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c3/1c3v_consurf.spt"</scriptWhenChecked>
1C3V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C3V OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
The three-dimensional structures of the Mycobacterium tuberculosis dihydrodipicolinate reductase-NADH-2,6-PDC and -NADPH-2,6-PDC complexes. Structural and mutagenic analysis of relaxed nucleotide specificity., Cirilli M, Zheng R, Scapin G, Blanchard JS, Biochemistry. 2003 Sep 16;42(36):10644-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12962488 12962488]
</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=1c3v ConSurf].
[[Category: Dihydrodipicolinate reductase]]
<div style="clear:both"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Mycobacterium tuberculosis]]
[[Category: Single protein]]
[[Category: Blanchard JS]]
[[Category: Blanchard, J S.]]
[[Category: Cirilli M]]
[[Category: Cirilli, M.]]
[[Category: Scapin G]]
[[Category: Scapin, G.]]
[[Category: Zheng R]]
[[Category: TBSGC, TB Structural Genomics Consortium.]]
[[Category: Zheng, R.]]
[[Category: NDP]]
[[Category: PDC]]
[[Category: PG4]]
[[Category: protein structure initiative]]
[[Category: psi]]
[[Category: structural genomic]]
[[Category: tb structural genomics consortium]]
[[Category: tbsgc]]
[[Category: two-domain structure]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:19:29 2008''
Retrieved from "https://proteopedia.org/1c3v"