2v5k

From Proteopedia

(Difference between revisions)

Current revision

Class II aldolase HpcH - magnesium - oxamate complex

Structural highlights

2v5k is a 2 chain structure with sequence from Escherichia coli C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.2Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

HPCH_ECOLX Catalyzes the reversible retro-aldol cleavage of 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) to pyruvate and succinate semialdehyde. Is also able to catalyze the aldol cleavage of 4-hydroxy-2-ketopentanoate and 4-hydroxy-2-ketohexanoate. Is not stereospecific since it can cleave both substrate enantiomers. Also exhibits significant oxaloacetate decarboxylase activity in vitro. In the reverse direction, is able to condense a range of aldehyde acceptors (from two to five carbons in length) with pyruvate or 2-oxobutanoate. Unlike with BphI from Burkholderia xenovorans, the aldol addition reaction lacks stereospecificity, producing a racemic mixture.^[1] ^[2]

Evolutionary Conservation

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

Publication Abstract from PubMed

Microorganisms are adept at degrading chemically resistant aromatic compounds. One of the longest and most well characterized aromatic catabolic pathways is the 4-hydroxyphenylacetic acid degradation pathway of Escherichia coli. The final step involves the conversion of 4-hydroxy-2-oxo-heptane-1,7-dioate into pyruvate and succinic semialdehyde. This reaction is catalyzed by 4-hydroxy-2-oxo-heptane-1,7-dioate aldolase (HpcH), a member of the divalent metal ion dependent class II aldolase enzymes that have great biosynthetic potential. We have solved the crystal structure of HpcH in the apo form, and with magnesium and the substrate analogue oxamate bound, to 1.6 A and 2.0 A, respectively. Comparison with similar structures of the homologous 2-dehydro-3-deoxygalactarate aldolase, coupled with site-directed mutagenesis data, implicate histidine 45 and arginine 70 as key catalytic residues.

Structure and mechanism of HpcH: a metal ion dependent class II aldolase from the homoprotocatechuate degradation pathway of Escherichia coli.,Rea D, Fulop V, Bugg TD, Roper DI J Mol Biol. 2007 Nov 2;373(4):866-76. Epub 2007 Jun 26. PMID:17881002^[3]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang W, Seah SY. Purification and biochemical characterization of a pyruvate-specific class II aldolase, HpaI. Biochemistry. 2005 Jul 12;44(27):9447-55. PMID:15996099 doi:10.1021/bi050607y
↑ Wang W, Baker P, Seah SY. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry. 2010 May 4;49(17):3774-82. PMID:20364820 doi:10.1021/bi100251u
↑ Rea D, Fulop V, Bugg TD, Roper DI. Structure and mechanism of HpcH: a metal ion dependent class II aldolase from the homoprotocatechuate degradation pathway of Escherichia coli. J Mol Biol. 2007 Nov 2;373(4):866-76. Epub 2007 Jun 26. PMID:17881002 doi:10.1016/j.jmb.2007.06.048

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2v5k"

@@ Line 3: / Line 3: @@
 <StructureSection load='2v5k' size='340' side='right'caption='[[2v5k]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2v5k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_c Escherichia coli c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V5K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2v5k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_C Escherichia coli C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V5K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V5K FirstGlance]. <br>
-</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=OXM:OXAMIC+ACID'>OXM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2v5j|2v5j]]</div></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=OXM:OXAMIC+ACID'>OXM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=2v5k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v5k OCA], [https://pdbe.org/2v5k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v5k RCSB], [https://www.ebi.ac.uk/pdbsum/2v5k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v5k ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/HPCH_ECOLX HPCH_ECOLX] Catalyzes the reversible retro-aldol cleavage of 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) to pyruvate and succinate semialdehyde. Is also able to catalyze the aldol cleavage of 4-hydroxy-2-ketopentanoate and 4-hydroxy-2-ketohexanoate. Is not stereospecific since it can cleave both substrate enantiomers. Also exhibits significant oxaloacetate decarboxylase activity in vitro. In the reverse direction, is able to condense a range of aldehyde acceptors (from two to five carbons in length) with pyruvate or 2-oxobutanoate. Unlike with BphI from Burkholderia xenovorans, the aldol addition reaction lacks stereospecificity, producing a racemic mixture.<ref>PMID:15996099</ref> <ref>PMID:20364820</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 34: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Escherichia coli c]]
+[[Category: Escherichia coli C]]
 [[Category: Large Structures]]
-[[Category: Bugg, T D.H]]
+[[Category: Bugg TDH]]
-[[Category: Fulop, V]]
+[[Category: Fulop V]]
-[[Category: Rea, D]]
+[[Category: Rea D]]
-[[Category: Roper, D I]]
+[[Category: Roper DI]]
-[[Category: Aromatic degradation]]
-[[Category: Aromatic hydrocarbons catabolismhomoprotocatechuate]]
-[[Category: Class ii aldolase]]
-[[Category: Homoprotocatechuate]]
-[[Category: Lyase]]

2v5k

From Proteopedia

Current revision

Class II aldolase HpcH - magnesium - oxamate complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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