1eli: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(15 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1eli.gif|left|200px]]<br /><applet load="1eli" size="350" color="white" frame="true" align="right" spinBox="true"
caption="1eli, resolution 2.00&Aring;" />
'''COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR PYRROLE-2-CARBOXYLATE'''<br />


==Overview==
==COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR PYRROLE-2-CARBOXYLATE==
Monomeric sarcosine oxidase (MSOX) is an inducible bacterial flavoenzyme that catalyzes the oxidative demethylation of sarcosine (N-methylglycine) and contains covalently bound FAD [8alpha-(S-cysteinyl)FAD]. This paper describes the spectroscopic and thermodynamic properties of MSOX as well as the X-ray crystallographic characterization of three new enzyme.inhibitor complexes. MSOX stabilizes the anionic form of the oxidized flavin (pK(a) = 8.3 versus 10.4 with free FAD), forms a thermodynamically stable flavin radical, and stabilizes the anionic form of the radical (pK(a) &lt; 6 versus pK(a) = 8.3 with free FAD). MSOX forms a covalent flavin.sulfite complex, but there appears to be a significant kinetic barrier against complex formation. Active site binding determinants were probed in thermodynamic studies with various substrate analogues whose binding was found to perturb the flavin absorption spectrum and inhibit MSOX activity. The carboxyl group of sarcosine is essential for binding since none is observed with simple amines. The amino group of sarcosine is not essential, but binding affinity depends on the nature of the substitution (CH(3)XCH(2)CO(2)(-), X = CH(2) &lt; O &lt; S &lt; Se &lt; Te), an effect which has been attributed to differences in the strength of donor-pi interactions. MSOX probably binds the zwitterionic form of sarcosine, as judged by the spectrally similar complexes formed with dimethylthioacetate [(CH(3))(2)S(+)CH(2)CO(2)(-)] and dimethylglycine (K(d) = 20.5 and 17.4 mM, respectively) and by the crystal structure of the latter. The methyl group of sarcosine is not essential but does contribute to binding affinity. The methyl group contribution varied from -3.79 to -0.65 kcal/mol with CH(3)XCH(2)CO(2)(-) depending on the nature of the heteroatom (NH(2)(+) &gt; O &gt; S) and appeared to be inversely correlated with heteroatom electron density. Charge-transfer complexes are formed with MSOX and CH(3)XCH(2)CO(2)(-) when X = S, Se, or Te. An excellent linear correlation is observed between the energy of the charge transfer bands and the one-electron reduction potentials of the ligands. The presence of a sulfur, selenium, or telurium atom identically positioned with respect to the flavin ring is confirmed by X-ray crystallography, although the increased atomic radius of S &lt; Se &lt; Te appears to simultaneously favor an alternate binding position for the heavier atoms. Although L-proline is a poor substrate, aromatic heterocyclic carboxylates containing a five-membered ring and various heteroatoms (X = NH, O, S) are good ligands (K(d, X=NH) = 1.37 mM) and form charge-transfer complexes with MSOX. The energy of the charge-transfer bands (S &gt; O &gt;&gt; NH) is linearly correlated with the one-electron ionization potentials of the corresponding heterocyclic rings.
<StructureSection load='1eli' size='340' side='right'caption='[[1eli]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1eli]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._B-0618 Bacillus sp. B-0618]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ELI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ELI 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&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYC:PYRROLE-2-CARBOXYLATE'>PYC</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=1eli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eli OCA], [https://pdbe.org/1eli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eli RCSB], [https://www.ebi.ac.uk/pdbsum/1eli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eli ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MSOX_BACB0 MSOX_BACB0] Catalyzes the oxidative demethylation of sarcosine. Can also oxidize other secondary amino acids such as N-methyl-L-alanine.[HAMAP-Rule:MF_00516]
== 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/el/1eli_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=1eli ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1ELI is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.] with <scene name='pdbligand=PO4:'>PO4</scene>, <scene name='pdbligand=CL:'>CL</scene>, <scene name='pdbligand=FAD:'>FAD</scene> and <scene name='pdbligand=PYC:'>PYC</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Sarcosine_oxidase Sarcosine oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.3.1 1.5.3.1] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ELI OCA].
*[[Sarcosine oxidase|Sarcosine oxidase]]
 
__TOC__
==Reference==
</StructureSection>
Monomeric sarcosine oxidase: 1. Flavin reactivity and active site binding determinants., Wagner MA, Trickey P, Chen ZW, Mathews FS, Jorns MS, Biochemistry. 2000 Aug 1;39(30):8813-24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10913292 10913292]
[[Category: Bacillus sp. B-0618]]
[[Category: Bacillus sp.]]
[[Category: Large Structures]]
[[Category: Sarcosine oxidase]]
[[Category: Chen Z-W]]
[[Category: Single protein]]
[[Category: Jorns MS]]
[[Category: Chen, Z W.]]
[[Category: Mathews FS]]
[[Category: Jorns, M S.]]
[[Category: Trickey P]]
[[Category: Mathews, F S.]]
[[Category: Wagner MA]]
[[Category: Trickey, P.]]
[[Category: Wagner, M A.]]
[[Category: CL]]
[[Category: FAD]]
[[Category: PO4]]
[[Category: PYC]]
[[Category: flavoprotein]]
[[Category: oxidase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:28:59 2008''

Latest revision as of 13:03, 20 March 2024

COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR PYRROLE-2-CARBOXYLATECOMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR PYRROLE-2-CARBOXYLATE

Structural highlights

1eli is a 2 chain structure with sequence from Bacillus sp. B-0618. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2Å
Ligands:, , , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

MSOX_BACB0 Catalyzes the oxidative demethylation of sarcosine. Can also oxidize other secondary amino acids such as N-methyl-L-alanine.[HAMAP-Rule:MF_00516]

Evolutionary Conservation

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

See Also

1eli, resolution 2.00Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=1eli&oldid=4108193"