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.

1yl7

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 15:02, 12 October 2017

the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)

Structural highlights

1yl7 is a 8 chain structure with sequence from "bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	1yl5, 1yl6
Gene:	dapB ("Bacillus tuberculosis" (Zopf 1883) Klein 1884)
Activity:	4-hydroxy-tetrahydrodipicolinate reductase, with EC number 1.17.1.8
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[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.^[1]

Evolutionary Conservation

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

Publication Abstract from PubMed

Dihydrodipicolinate reductase (DHDPR, DapB) is an enzyme that belongs to the L-lysine biosynthetic pathway. DHDPR reduces the alpha,beta-unsaturated cyclic imine 2,3-dihydrodipicolinic acid to yield the compound 2,3,4,5-tetrahydrodipicolinic acid in a pyridine nucleotide-dependent reaction. The substrate of this reaction is the unstable product of the preceding enzyme dihydrodipicolinate synthase (DHDPS, DapA). Here, the structure of apo-DHDPR from Mycobacterium tuberculosis is reported in two orthorhombic crystal forms, as well as the structure of DHDPR from M. tuberculosis in complex with NADH in a monoclinic crystal form. A comparison of the results with previously solved structures of this enzyme shows that DHDPR undergoes a major conformational change upon binding of its cofactor. This conformational change can be interpreted as one of the low-frequency normal modes of the structure.

The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms.,Janowski R, Kefala G, Weiss MS Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):61-72. Epub 2009, Dec 21. PMID:20057050^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Cirilli M, Zheng R, Scapin G, Blanchard JS. 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. Biochemistry. 2003 Sep 16;42(36):10644-50. PMID:12962488 doi:http://dx.doi.org/10.1021/bi030044v
↑ Janowski R, Kefala G, Weiss MS. The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms. Acta Crystallogr D Biol Crystallogr. 2010 Jan;66(Pt 1):61-72. Epub 2009, Dec 21. PMID:20057050 doi:10.1107/S0907444909043960

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1yl7"

@@ Line 1: / Line 1: @@
 ==the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)==
 <StructureSection load='1yl7' size='340' side='right' caption='[[1yl7]], [[Resolution|resolution]] 2.34&Aring;' scene=''>
@@ Line 7: / Line 8: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">dapB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/4-hydroxy-tetrahydrodipicolinate_reductase 4-hydroxy-tetrahydrodipicolinate reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.17.1.8 1.17.1.8] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yl7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yl7 OCA], [http://pdbe.org/1yl7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yl7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yl7 PDBsum], [http://www.topsan.org/Proteins/TBSGC/1yl7 TOPSAN]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1yl7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yl7 OCA], [http://pdbe.org/1yl7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1yl7 RCSB], [http://www.ebi.ac.uk/pdbsum/1yl7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1yl7 ProSAT], [http://www.topsan.org/Proteins/TBSGC/1yl7 TOPSAN]</span></td></tr>
 </table>
 == Function ==

1yl7

From Proteopedia

Revision as of 15:02, 12 October 2017

the crystal structure of Mycobacterium tuberculosis dihydrodipicolinate reductase (Rv2773c) in complex with NADH (crystal form C)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox