2v2a: Difference between revisions

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Revision as of 19:42, 20 March 2008

File:2v2a.jpg

, resolution 1.75Å

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, and

Ligands:

and

Activity:

Rhamnulose-1-phosphate aldolase, with EC number 4.1.2.19

Coordinates:

save as pdb, mmCIF, xml

L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248G-R253A-E254A)

OverviewOverview

The enzyme l-rhamnulose-1-phosphate aldolase from Escherichia coli participates in the degradation pathway of l-rhamnose, a ubiquitous deoxy-hexose. It is a homotetramer of the rare C4-symmetric type with N-terminal domains protruding like antennas from the main body. A mobility analysis of the enzyme gave rise to the hypothesis that an anisotropic thermal antenna motion may support the catalysis (Kroemer et al., Biochemistry 42, 10560, 2003). We checked this hypothesis by generating four single mutants and one disulfide bridge that were designed to reduce the mobility of the antenna domain without disturbing the chain-fold or the active center. The catalytic rates of the mutants revealed activity reductions that correlated well with the expected antenna fixation. Among these mutants, K15W was crystallized, structurally elucidated, and used as a guide for modeling the others. The structure confirmed the design because the mutation introduced a tight nonpolar contact to a neighboring subunit that fixed the antenna but did not affect the main chain. The fixation was confirmed by a comparison of the anisotropic B-factors describing the mobility of the domains. It turned out that the distinctly anisotropic mobility of the wild-type antenna domain has become isotropic in K15W, in agreement with the design. We suggest that, like K15W, the other mutations also followed the design, validating the correlation between antenna mobility and activity. This correlation suggests that the domain mobility facilitates the reaction.

About this StructureAbout this Structure

2V2A is a Single protein structure of sequence from Escherichia coli. Full crystallographic information is available from OCA.

ReferenceReference

Antenna domain mobility and enzymatic reaction of L-rhamnulose-1-phosphate aldolase., Grueninger D, Schulz GE, Biochemistry. 2008 Jan 15;47(2):607-14. Epub 2007 Dec 18. PMID:18085797

Page seeded by OCA on Thu Mar 20 18:42:36 2008

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

OCA

@@ Line 1: / Line 1: @@
-[[Image:2v2a.jpg|left|200px]]<br /><applet load="2v2a" size="350" color="white" frame="true" align="right" spinBox="true"
+[[Image:2v2a.jpg|left|200px]]
-caption="2v2a, resolution 1.75&Aring;" />
-'''L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248G-R253A-E254A)'''<br />
+ {{Structure
+|PDB= 2v2a |SIZE=350|CAPTION= <scene name='initialview01'>2v2a</scene>, resolution 1.75&Aring;
+|SITE= <scene name='pdbsite=AC1:Zn+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Zn+Binding+Site+For+Chain+A'>AC2</scene> and <scene name='pdbsite=AC3:13p+Binding+Site+For+Chain+A'>AC3</scene>
+|LIGAND= <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene> and <scene name='pdbligand=13P:1,3-DIHYDROXYACETONEPHOSPHATE'>13P</scene>
+|ACTIVITY= [http://en.wikipedia.org/wiki/Rhamnulose-1-phosphate_aldolase Rhamnulose-1-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.19 4.1.2.19]
+|GENE=
+}}
+'''L-RHAMNULOSE-1-PHOSPHATE ALDOLASE FROM ESCHERICHIA COLI (MUTANT E192A-K248G-R253A-E254A)'''
 ==Overview==
@@ Line 7: / Line 16: @@
 ==About this Structure==
-V2A is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with <scene name='pdbligand=ZN:'>ZN</scene> and <scene name='pdbligand=13P:'>13P</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Rhamnulose-1-phosphate_aldolase Rhamnulose-1-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.19 4.1.2.19] Known structural/functional Sites: <scene name='pdbsite=AC1:Zn+Binding+Site+For+Chain+A'>AC1</scene>, <scene name='pdbsite=AC2:Zn+Binding+Site+For+Chain+A'>AC2</scene> and <scene name='pdbsite=AC3:13p+Binding+Site+For+Chain+A'>AC3</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2V2A OCA].
+V2A 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=2V2A OCA].
 ==Reference==
-Antenna domain mobility and enzymatic reaction of L-rhamnulose-1-phosphate aldolase., Grueninger D, Schulz GE, Biochemistry. 2008 Jan 15;47(2):607-14. Epub 2007 Dec 18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18085797 18085797]
+Antenna domain mobility and enzymatic reaction of L-rhamnulose-1-phosphate aldolase., Grueninger D, Schulz GE, Biochemistry. 2008 Jan 15;47(2):607-14. Epub 2007 Dec 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18085797 18085797]
 [[Category: Escherichia coli]]
 [[Category: Rhamnulose-1-phosphate aldolase]]
@@ Line 34: / Line 43: @@
 [[Category: zinc enzyme]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:52:39 2008''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:42:36 2008''