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.


1bwz

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:36, 13 March 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1bwz.gif|left|200px]]<br /><applet load="1bwz" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1bwz, resolution 2.72&Aring;" />
 
-
'''DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE'''<br />
 
-
==Overview==
+
==DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE==
-
The Haemophilus influenzae diaminopimelate epimerase was cloned, expressed, purified, and crystallized in the C2221 space group (a = 102.1 A, b = 115.4 A, c = 66.3 A, alpha = beta = gamma = 90 degrees). The three-dimensional structure was solved to 2.7 A using a single Pt derivative and the Se-Met-substituted enzyme to a conventional R factor of 19.0% (Rfree = 24.2%). The 274 amino acid enzyme consists of two structurally homologous domains, each containing eight beta-strands and two alpha-helices. Diaminopimelate epimerase is a representative of the PLP-independent amino acid racemases, for which no structure has yet been determined and substantial evidence exists supporting the role of two cysteine residues as the catalytic acid and base. Cys73 of the amino terminal domain is found in disulfide linkage, at the domain interface, with Cys217 of the carboxy terminal domain, and we suggest that these two cysteine residues in the reduced, active enzyme function as the acid and base in the mechanism.
+
<StructureSection load='1bwz' size='340' side='right'caption='[[1bwz]], [[Resolution|resolution]] 2.72&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1bwz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BWZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BWZ FirstGlance]. <br>
-
1BWZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Haemophilus_influenzae Haemophilus influenzae]. Active as [http://en.wikipedia.org/wiki/Diaminopimelate_epimerase Diaminopimelate epimerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=5.1.1.7 5.1.1.7] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BWZ 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]] 2.72&#8491;</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=1bwz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bwz OCA], [https://pdbe.org/1bwz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bwz RCSB], [https://www.ebi.ac.uk/pdbsum/1bwz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bwz ProSAT]</span></td></tr>
-
==Reference==
+
</table>
-
Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase., Cirilli M, Zheng R, Scapin G, Blanchard JS, Biochemistry. 1998 Nov 24;37(47):16452-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9843410 9843410]
+
== Function ==
-
[[Category: Diaminopimelate epimerase]]
+
[https://www.uniprot.org/uniprot/DAPF_HAEIN DAPF_HAEIN] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. Only accepts DAP isomers with the L configuration.<ref>PMID:10194362</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/bw/1bwz_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=1bwz ConSurf].
 +
<div style="clear:both"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Haemophilus influenzae]]
[[Category: Haemophilus influenzae]]
-
[[Category: Single protein]]
+
[[Category: Large Structures]]
-
[[Category: Blanchard, J S.]]
+
[[Category: Blanchard JS]]
-
[[Category: Cirilli, M.]]
+
[[Category: Cirilli M]]
-
[[Category: Scapin, G.]]
+
[[Category: Scapin G]]
-
[[Category: Zheng, R.]]
+
[[Category: Zheng R]]
-
[[Category: metabolic role]]
+
-
[[Category: structural classification]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:00:03 2008''
+

Current revision

DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE

PDB ID 1bwz

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/1bwz"
Personal tools