3bi1: Difference between revisions

Revision as of 20:47, 4 May 2008

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a transition state analog of methotrexate-Glu

OverviewOverview

Human glutamate carboxypeptidase II (GCPII) is involved in neuronal signal transduction and intestinal folate absorption by means of the hydrolysis of its two natural substrates, N-acetyl-aspartyl-glutamate and folyl-poly-gamma-glutamates, respectively. During the past years, tremendous efforts have been made toward the structural analysis of GCPII. Crystal structures of GCPII in complex with various ligands have provided insight into the binding of these ligands, particularly to the S1' site of the enzyme. In this article, we have extended structural characterization of GCPII to its S1 site by using dipeptide-based inhibitors that interact with both S1 and S1' sites of the enzyme. To this end, we have determined crystal structures of human GCPII in complex with phosphapeptide analogs of folyl-gamma-glutamate, aspartyl-glutamate, and gamma-glutamyl-glutamate, refined at 1.50, 1.60, and 1.67 A resolution, respectively. The S1 pocket of GCPII could be accurately defined and analyzed for the first time, and the data indicate the importance of Asn519, Arg463, Arg534, and Arg536 for recognition of the penultimate (i.e., P1) substrate residues. Direct interactions between the positively charged guanidinium groups of Arg534 and Arg536 and a P1 moiety of a substrate/inhibitor provide mechanistic explanation of GCPII preference for acidic dipeptides. Additionally, observed conformational flexibility of the Arg463 and Arg536 side chains likely regulates GCPII affinity toward different inhibitors and modulates GCPII substrate specificity. The biochemical experiments assessing the hydrolysis of several GCPII substrate derivatives modified at the P1 position, also included in this report, further complement and extend conclusions derived from the structural analysis. The data described here form an a solid foundation for the structurally aided design of novel low-molecular-weight GCPII inhibitors and imaging agents.

About this StructureAbout this Structure

3BI1 is a Single protein structure of sequence from Homo sapiens. Full crystallographic information is available from OCA.

ReferenceReference

Structural basis of interactions between human glutamate carboxypeptidase II and its substrate analogs., Barinka C, Hlouchova K, Rovenska M, Majer P, Dauter M, Hin N, Ko YS, Tsukamoto T, Slusher BS, Konvalinka J, Lubkowski J, J Mol Biol. 2008 Mar 7;376(5):1438-50. Epub 2008 Jan 5. PMID:18234225 Page seeded by OCA on Sun May 4 20:47:21 2008

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OCA

@@ Line 1: / Line 1: @@
 [[Image:3bi1.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 3bi1 |SIZE=350|CAPTION= <scene name='initialview01'>3bi1</scene>, resolution 1.50&Aring;
+The line below this paragraph, containing "STRUCTURE_3bi1", creates the "Structure Box" on the page.
-|SITE= <scene name='pdbsite=AC1:Nag+Binding+Site+For+Residue+A+1755'>AC1</scene>, <scene name='pdbsite=AC2:Nag+Binding+Site+For+Residue+A+1756'>AC2</scene>, <scene name='pdbsite=AC3:Nag+Binding+Site+For+Residue+A+1757'>AC3</scene>, <scene name='pdbsite=AC4:Nag+Binding+Site+For+Residue+A+1758'>AC4</scene>, <scene name='pdbsite=AC5:Nag+Binding+Site+For+Residue+A+1759'>AC5</scene>, <scene name='pdbsite=AC6:Nag+Binding+Site+For+Residue+A+1760'>AC6</scene>, <scene name='pdbsite=AC7:Nag+Binding+Site+For+Residue+A+1761'>AC7</scene>, <scene name='pdbsite=AC8:Nag+Binding+Site+For+Residue+A+1762'>AC8</scene>, <scene name='pdbsite=AC9:Nag+Binding+Site+For+Residue+A+1763'>AC9</scene>, <scene name='pdbsite=BC1:Nag+Binding+Site+For+Residue+A+1764'>BC1</scene>, <scene name='pdbsite=BC2:Bma+Binding+Site+For+Residue+A+1765'>BC2</scene>, <scene name='pdbsite=BC3:Man+Binding+Site+For+Residue+A+1766'>BC3</scene>, <scene name='pdbsite=BC4:Zn+Binding+Site+For+Residue+A+1751'>BC4</scene>, <scene name='pdbsite=BC5:Zn+Binding+Site+For+Residue+A+1752'>BC5</scene>, <scene name='pdbsite=BC6:Ca+Binding+Site+For+Residue+A+1753'>BC6</scene>, <scene name='pdbsite=BC7:Cl+Binding+Site+For+Residue+A+1754'>BC7</scene> and <scene name='pdbsite=BC8:3bi+Binding+Site+For+Residue+A+1'>BC8</scene>
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=3BI:(2S)-2-{[(R)-[(3R)-3-CARBOXY-3-{[(4-{[(2,4-DIAMINOPTERIDIN-6-YL)METHYL](METHYL)AMINO}PHENYL)CARBONYL]AMINO}PROPYL](HYDROXY)PHOSPHORYL]METHYL}PENTANEDIOIC+ACID'>3BI</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_carboxypeptidase_II Glutamate carboxypeptidase II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.17.21 3.4.17.21] </span>
+or leave the SCENE parameter empty for the default display.
-|GENE= FOLH1, FOLH, NAALAD1, PSM, PSMA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])
+-->
-|DOMAIN=
+{{STRUCTURE_3bi1|  PDB=3bi1  |  SCENE=  }}
-|RELATEDENTRY=[[3bi0|3BI0]], [[3bhx|3BHX]]
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3bi1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3bi1 OCA], [http://www.ebi.ac.uk/pdbsum/3bi1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=3bi1 RCSB]</span>
-}}
 '''X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a transition state analog of methotrexate-Glu'''
@@ Line 28: / Line 25: @@
 [[Category: Barinka, C.]]
 [[Category: Lubkowski, J.]]
-[[Category: alternative splicing]]
+[[Category: Alternative splicing]]
-[[Category: cytoplasm]]
+[[Category: Cytoplasm]]
-[[Category: dipeptidase]]
+[[Category: Dipeptidase]]
-[[Category: folate hydrolase]]
+[[Category: Folate hydrolase]]
-[[Category: glutamate carboxypeptidase ii]]
+[[Category: Glutamate carboxypeptidase ii]]
-[[Category: glycoprotein]]
+[[Category: Glycoprotein]]
-[[Category: metal-binding]]
+[[Category: Metal-binding]]
-[[Category: metallopeptidase]]
+[[Category: Metallopeptidase]]
-[[Category: metalloprotease]]
+[[Category: Metalloprotease]]
-[[Category: multifunctional enzyme]]
+[[Category: Multifunctional enzyme]]
-[[Category: naaladase]]
+[[Category: Naaladase]]
-[[Category: polymorphism]]
+[[Category: Polymorphism]]
-[[Category: prostate specific membrane antigen]]
+[[Category: Prostate specific membrane antigen]]
-[[Category: protease]]
+[[Category: Protease]]
-[[Category: signal-anchor]]
+[[Category: Signal-anchor]]
-[[Category: transmembrane]]
+[[Category: Transmembrane]]
-[[Category: zinc]]
+[[Category: Zinc]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 20:47:21 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:26:26 2008''