1fdz: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
 
(16 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:1fdz.gif|left|200px]]


{{Structure
==N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH PYRUVATE VIA BOROHYDRIDE REDUCTION==
|PDB= 1fdz |SIZE=350|CAPTION= <scene name='initialview01'>1fdz</scene>, resolution 2.6&Aring;
<StructureSection load='1fdz' size='340' side='right'caption='[[1fdz]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=PYR:PYRUVIC ACID'>PYR</scene>
<table><tr><td colspan='2'>[[1fdz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FDZ FirstGlance]. <br>
|ACTIVITY= [http://en.wikipedia.org/wiki/N-acetylneuraminate_lyase N-acetylneuraminate lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.3.3 4.1.3.3]  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
|GENE= NPL ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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=1fdz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fdz OCA], [https://pdbe.org/1fdz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fdz RCSB], [https://www.ebi.ac.uk/pdbsum/1fdz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fdz ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NANA_ECOLI NANA_ECOLI] Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate.[HAMAP-Rule:MF_01237]
== 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/fd/1fdz_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1fdz ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We describe here a sub-family of enzymes related both structurally and functionally to N-acetylneuraminate lyase. Two members of this family (N-acetylneuraminate lyase and dihydrodipicolinate synthase) have known three-dimensional structures and we now proceed to show their structural and functional relationship to two further proteins, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase and D-4-deoxy-5-oxoglucarate dehydratase. These enzymes are all thought to involve intermediate Schiff-base formation with their respective substrates. In order to understand the nature of this intermediate, we have determined the three-dimensional structure of N-acetylneuraminate lyase in complex with hydroxypyruvate (a product analogue) and in complex with one of its products (pyruvate). From these structures we deduce the presence of a closely similar Schiff-base forming motif in all members of the N-acetylneuraminate lyase sub-family. A fifth protein, MosA, is also confirmed to be a member of the sub-family although the involvement of an intermediate Schiff-base in its proposed reaction is unclear.


'''N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH PYRUVATE VIA BOROHYDRIDE REDUCTION'''
Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase.,Lawrence MC, Barbosa JA, Smith BJ, Hall NE, Pilling PA, Ooi HC, Marcuccio SM J Mol Biol. 1997 Feb 21;266(2):381-99. PMID:9047371<ref>PMID:9047371</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1fdz" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
We describe here a sub-family of enzymes related both structurally and functionally to N-acetylneuraminate lyase. Two members of this family (N-acetylneuraminate lyase and dihydrodipicolinate synthase) have known three-dimensional structures and we now proceed to show their structural and functional relationship to two further proteins, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase and D-4-deoxy-5-oxoglucarate dehydratase. These enzymes are all thought to involve intermediate Schiff-base formation with their respective substrates. In order to understand the nature of this intermediate, we have determined the three-dimensional structure of N-acetylneuraminate lyase in complex with hydroxypyruvate (a product analogue) and in complex with one of its products (pyruvate). From these structures we deduce the presence of a closely similar Schiff-base forming motif in all members of the N-acetylneuraminate lyase sub-family. A fifth protein, MosA, is also confirmed to be a member of the sub-family although the involvement of an intermediate Schiff-base in its proposed reaction is unclear.
*[[N-acetylneuraminate lyase 3D structures|N-acetylneuraminate lyase 3D structures]]
 
== References ==
==About this Structure==
<references/>
1FDZ is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FDZ OCA].
__TOC__
 
</StructureSection>
==Reference==
Structure and mechanism of a sub-family of enzymes related to N-acetylneuraminate lyase., Lawrence MC, Barbosa JA, Smith BJ, Hall NE, Pilling PA, Ooi HC, Marcuccio SM, J Mol Biol. 1997 Feb 21;266(2):381-99. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9047371 9047371]
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: N-acetylneuraminate lyase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Barbosa JARG]]
[[Category: Barbosa, J A.R G.]]
[[Category: Hall NE]]
[[Category: Hall, N E.]]
[[Category: Lawrence MC]]
[[Category: Lawrence, M C.]]
[[Category: Marcuccio SM]]
[[Category: Marcuccio, S M.]]
[[Category: Ooi HC]]
[[Category: Ooi, H C.]]
[[Category: Pilling PA]]
[[Category: Pilling, P A.]]
[[Category: Smith BJ]]
[[Category: Smith, B J.]]
[[Category: PYR]]
[[Category: aldolase]]
[[Category: alpha-keto-acid lyase]]
[[Category: carbon-carbon lyase]]
[[Category: lyase]]
[[Category: oxo-acid lyase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:07:52 2008''

Latest revision as of 04:31, 17 October 2024

N-ACETYLNEURAMINATE LYASE IN COMPLEX WITH PYRUVATE VIA BOROHYDRIDE REDUCTION

1fdz, resolution 2.60Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "https://proteopedia.org/index.php?title=1fdz&oldid=4223318"