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1wyt

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Revision as of 16:18, 11 April 2018

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in apo form

Structural highlights

1wyt is a 4 chain structure with sequence from Thet8. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1wyu, 1wyv
Gene:	GCSA (THET8), GCSB (THET8)
Activity:	Glycine dehydrogenase (decarboxylating), with EC number 1.4.4.2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[Q5SKW8_THET8] The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein (By similarity).[HAMAP-Rule:MF_00712][SAAS:SAAS023010_004_045580] [GCSPB_THET8] The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO(2) is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein (By similarity).

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

The crystal structure of the P-protein of the glycine cleavage system from Thermus thermophilus HB8 has been determined. This is the first reported crystal structure of a P-protein, and it reveals that P-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (PLP)-dependent enzymes. Instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally similar and appear to have arisen by gene duplication and subsequent divergence with a loss of one active site. The binding of PLP to the apoenzyme induces large open-closed conformational changes, with residues moving up to 13.5 A. The structure of the complex formed by the holoenzyme bound to an inhibitor, (aminooxy)acetate, suggests residues that may be responsible for substrate recognition. The molecular surface around the lipoamide-binding channel shows conservation of positively charged residues, which are possibly involved in complex formation with the H-protein. These results provide insights into the molecular basis of nonketotic hyperglycinemia.

Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia.,Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N EMBO J. 2005 Apr 20;24(8):1523-36. Epub 2005 Mar 24. PMID:15791207^[1]

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

References

↑ Nakai T, Nakagawa N, Maoka N, Masui R, Kuramitsu S, Kamiya N. Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia. EMBO J. 2005 Apr 20;24(8):1523-36. Epub 2005 Mar 24. PMID:15791207

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1wyt"

@@ Line 1: / Line 1: @@
 ==Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in apo form==
 <StructureSection load='1wyt' size='340' side='right' caption='[[1wyt]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
@@ Line 6: / Line 7: @@
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GCSA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8]), GCSB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=300852 THET8])</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_dehydrogenase_(decarboxylating) Glycine dehydrogenase (decarboxylating)], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.4.2 1.4.4.2] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyt OCA], [http://pdbe.org/1wyt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wyt RCSB], [http://www.ebi.ac.uk/pdbsum/1wyt PDBsum], [http://www.topsan.org/Proteins/RSGI/1wyt TOPSAN]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1wyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wyt OCA], [http://pdbe.org/1wyt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wyt RCSB], [http://www.ebi.ac.uk/pdbsum/1wyt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wyt ProSAT], [http://www.topsan.org/Proteins/RSGI/1wyt TOPSAN]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyt_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wy/1wyt_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=1wyt ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">

1wyt

From Proteopedia

Revision as of 16:18, 11 April 2018

Crystal structure of glycine decarboxylase (P-protein) of the glycine cleavage system, in apo form

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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