1bpm

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:38, 7 February 2024) (edit) (undo)
 
(18 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1bpm.jpg|left|200px]]<br /><applet load="1bpm" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1bpm, resolution 2.9&Aring;" />
 
-
'''DIFFERENTIATION AND IDENTIFICATION OF THE TWO CATALYTIC METAL BINDING SITES IN BOVINE LENS LEUCINE AMINOPEPTIDASE BY X-RAY CRYSTALLOGRAPHY'''<br />
 
-
==Overview==
+
==DIFFERENTIATION AND IDENTIFICATION OF THE TWO CATALYTIC METAL BINDING SITES IN BOVINE LENS LEUCINE AMINOPEPTIDASE BY X-RAY CRYSTALLOGRAPHY==
-
The tightly binding and readily exchanging metal binding sites in the active site of bovine lens leucine aminopeptidase (blLAP; EC 3.4.11.1) have been differentiated and identified by x-ray crystallography. In native blLAP,Zn2+ occupies both binding sites. In solution, site 1 readily exchanges Zn2+ for other divalent cations, including Mg2+. The Zn2+ in site 2 is unavailable for metal exchange under conditions which allow exchange at site 1. The Zn2+/Mg2+ metal hybrid of blLAP (Mg-blLAP) was prepared in solution and crystallized. X-ray diffraction data to 2.9-A resolution were collected at -150 degrees C from single crystals of Mg-blLAP and native blLAP. Comparisons of omit maps calculated from the Mg-blLAP data with analogous maps calculated from the native blLAP data show electron density in one of the metal binding sites in Mg-blLAP which is much weaker than the electron density in the other binding site. Since there are fewer electrons associated with Mg2+ than with Zn2+, the difference in electron density between the two metal binding sites is consistent with occupancy of the weaker electron density site by Mg2+ and identifies this metal binding site as site 1, defined as the readily exchanging site. The present identification of the metal binding sites reverses the previous presumptive assignment of the metal binding sites which was based on the structure of native blLAP [Burley, S. K., David, P. R., Sweet, R. M., Taylor, A. &amp; Lipscomb, W. N. (1992) J. Mol. Biol. 224, 113-140]. According to the residue-numbering convention of native blLAP, the new assignment of the metal binding sites identifies the readily exchanging site 1 with Zn-488, which is within interaction distance of one side-chain carboxylate oxygen from each of Asp-255, Asp-332, and Glu-334 and the main-chain carbonyl oxygen of Asp-332. The more tightly binding site 2 is identified with Zn-489, which is within interaction distance of one side-chain carboxylate oxygen from each of Asp-255, Asp-273, and Glu-334 and the side-chain amine nitrogen of Lys-250.
+
<StructureSection load='1bpm' size='340' side='right'caption='[[1bpm]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1bpm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BPM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BPM FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1bpm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bpm OCA], [https://pdbe.org/1bpm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bpm RCSB], [https://www.ebi.ac.uk/pdbsum/1bpm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bpm ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/AMPL_BOVIN AMPL_BOVIN] Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides.
 +
== 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/bp/1bpm_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=1bpm ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1BPM is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=ZN:'>ZN</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Leucyl_aminopeptidase Leucyl aminopeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.1 3.4.11.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BPM OCA].
+
*[[Aminopeptidase 3D structures|Aminopeptidase 3D structures]]
-
 
+
__TOC__
-
==Reference==
+
</StructureSection>
-
Differentiation and identification of the two catalytic metal binding sites in bovine lens leucine aminopeptidase by x-ray crystallography., Kim H, Lipscomb WN, Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5006-10. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8506345 8506345]
+
[[Category: Bos taurus]]
-
[[Category: Leucyl aminopeptidase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[Category: Kim H]]
-
[[Category: Kim, H.]]
+
[[Category: Lipscomb WN]]
-
[[Category: Lipscomb, W N.]]
+
-
[[Category: MG]]
+
-
[[Category: ZN]]
+
-
[[Category: hydrolase(alpha-aminoacylpeptide)]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:57:48 2008''
+

Current revision

DIFFERENTIATION AND IDENTIFICATION OF THE TWO CATALYTIC METAL BINDING SITES IN BOVINE LENS LEUCINE AMINOPEPTIDASE BY X-RAY CRYSTALLOGRAPHY

PDB ID 1bpm

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/1bpm"
Personal tools