1ddk: Difference between revisions

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New page: left|200px<br /><applet load="1ddk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ddk, resolution 3.10Å" /> '''CRYSTAL STRUCTURE OF...
 
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[[Image:1ddk.gif|left|200px]]<br /><applet load="1ddk" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1ddk, resolution 3.10&Aring;" />
'''CRYSTAL STRUCTURE OF IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA'''<br />


==Overview==
==CRYSTAL STRUCTURE OF IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA==
Metallo beta-lactamase enzymes confer antibiotic resistance to bacteria by, catalyzing the hydrolysis of beta-lactam antibiotics. This relatively new, form of resistance is spreading unchallenged as there is a current lack of, potent and selective inhibitors of metallo beta-lactamases. Reported here, are the crystal structures of the native IMP-1 metallo beta-lactamase from, Pseudomonas aeruginosa and its complex with a mercaptocarboxylate, inhibitor, 2-[5-(1-tetrazolylmethyl)thien-3-yl]-N-[2-(mercaptomethyl)-4, -(phenylb utyrylglycine)]. The structures were determined by molecular, replacement, and refined to 3.1 A (native) and 2.0 A (complex) resolution., Binding of the inhibitor in the active site induces a conformational, change that results in closing of the flap and transforms the active site, groove into a tunnel-shaped cavity enclosing 83% of the solvent accessible, surface area of the inhibitor. The inhibitor binds in the active site, through interactions with residues that are conserved among metallo, beta-lactamases; the inhibitor's carboxylate group interacts with Lys161, and the main chain amide nitrogen of Asn167. In the "oxyanion hole", the, amide carbonyl oxygen of the inhibitor interacts through a water molecule, with the side chain of Asn167, the inhibitor's thiolate bridges the two, Zn(II) ions in the active site displacing the bridging water, and the, phenylbutyryl side chain binds in a hydrophobic pocket (S1) at the base of, the flap. The flap is displaced 2.9 A compared to the unbound structure, allowing Trp28 to interact edge-to-face with the inhibitor's thiophene, ring. The similarities between this inhibitor and the beta-lactam, substrates suggest a mode of substrate binding and the role of the, conserved residues in the active site. It appears that the metallo, beta-lactamases bind their substrates by establishing a subset of binding, interactions near the catalytic center with conserved characteristic, chemical groups of the beta-lactam substrates. These interactions are, complemented by additional nonspecific binding between the more variable, groups in the substrates and the flexible flap. This unique mode of, binding of the mercaptocarboxylate inhibitor in the enzyme active site, provides a binding model for metallo beta-lactamase inhibition with, utility for future drug design.
<StructureSection load='1ddk' size='340' side='right'caption='[[1ddk]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1ddk]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DDK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DDK 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]] 3.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</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=1ddk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ddk OCA], [https://pdbe.org/1ddk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ddk RCSB], [https://www.ebi.ac.uk/pdbsum/1ddk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ddk ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/Q79MP6_PSEAI Q79MP6_PSEAI]
== 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/dd/1ddk_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=1ddk ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1DDK is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa] with ZN and ACY as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DDK OCA].
*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
Crystal structure of the IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor: binding determinants of a potent, broad-spectrum inhibitor., Concha NO, Janson CA, Rowling P, Pearson S, Cheever CA, Clarke BP, Lewis C, Galleni M, Frere JM, Payne DJ, Bateson JH, Abdel-Meguid SS, Biochemistry. 2000 Apr 18;39(15):4288-98. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10757977 10757977]
[[Category: Large Structures]]
[[Category: Beta-lactamase]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Pseudomonas aeruginosa]]
[[Category: Single protein]]
[[Category: Abdel-Meguid SS]]
[[Category: Abdel-Meguid, S.S.]]
[[Category: Bateson JH]]
[[Category: Bateson, J.H.]]
[[Category: Cheever CA]]
[[Category: Cheever, C.A.]]
[[Category: Clarke BP]]
[[Category: Clarke, B.P.]]
[[Category: Concha NO]]
[[Category: Concha, N.O.]]
[[Category: Frere JM]]
[[Category: Frere, J.M.]]
[[Category: Galleni M]]
[[Category: Galleni, M.]]
[[Category: Janson CA]]
[[Category: Janson, C.A.]]
[[Category: Lewis C]]
[[Category: Lewis, C.]]
[[Category: Payne DJ]]
[[Category: Payne, D.J.]]
[[Category: Pearson S]]
[[Category: Pearson, S.]]
[[Category: Rowling P]]
[[Category: Rowling, P.]]
[[Category: ACY]]
[[Category: ZN]]
[[Category: binuclear metal center]]
[[Category: imp-1 metallo beta-lactamase]]
[[Category: x-ray crystallography]]
[[Category: zn beta-lactamase]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:00:31 2007''

Latest revision as of 09:52, 7 February 2024

CRYSTAL STRUCTURE OF IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSACRYSTAL STRUCTURE OF IMP-1 METALLO BETA-LACTAMASE FROM PSEUDOMONAS AERUGINOSA

Structural highlights

1ddk is a 1 chain structure with sequence from Pseudomonas aeruginosa. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.1Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Q79MP6_PSEAI

Evolutionary Conservation

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

See Also

1ddk, resolution 3.10Å

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