This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1g2p

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

CRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE

Structural highlights

1g2p is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.75Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

APT1_YEAST Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.^[1]

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

Adenine phosphoribosyltransferase (APRTase) is a widely distributed enzyme, and its deficiency in humans causes the accumulation of 2,8-dihydroxyadenine. It is the sole catalyst for adenine recycling in most eukaryotes. The most commonly expressed APRTase has subunits of approximately 187 amino acids, but the only crystal structure is from Leishmania donovani, which expresses a long form of the enzyme with 237 residues. Saccharomyces cerevisiae APRTase was selected as a representative of the short APRTases, and the structure of the apo-enzyme and sulfate bound forms were solved to 1.5 and 1.75 A, respectively. Yeast APRTase is a dimeric molecule, and each subunit is composed of a central five-stranded beta-sheet surrounded by five alpha-helices, a structural theme found in all known purine phosphoribosyltransferases. The structures reveal several important features of APRTase function: (i) sulfate ions bound at the 5'-phosphate and pyrophosphate binding sites; (ii) a nonproline cis peptide bond (Glu67-Ser68) at the pyrophosphate binding site in both apo-enzyme and sulfate-bound forms; and (iii) a catalytic loop that is open and ordered in the apo-enzyme but open and disordered in the sulfate-bound form. Alignment of conserved amino acids in short-APRTases from 33 species reveals 13 invariant and 15 highly conserved residues present in hinges, catalytic site loops, and the catalytic pocket. Mutagenesis of conserved residues in the catalytic loop, subunit interface, and phosphoribosylpyrophosphate binding site indicates critical roles for the tip of the catalytic loop (Glu106) and a catalytic site residue Arg69, respectively. Mutation of one loop residue (Tyr103Phe) increases k(cat) by 4-fold, implicating altered dynamics for the catalytic site loop.

Structural analysis of adenine phosphoribosyltransferase from Saccharomyces cerevisiae.,Shi W, Tanaka KS, Crother TR, Taylor MW, Almo SC, Schramm VL Biochemistry. 2001 Sep 11;40(36):10800-9. PMID:11535055^[2]

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

References

↑ Alfonzo JD, Crother TR, Guetsova ML, Daignan-Fornier B, Taylor MW. APT1, but not APT2, codes for a functional adenine phosphoribosyltransferase in Saccharomyces cerevisiae. J Bacteriol. 1999 Jan;181(1):347-52. PMID:9864350
↑ Shi W, Tanaka KS, Crother TR, Taylor MW, Almo SC, Schramm VL. Structural analysis of adenine phosphoribosyltransferase from Saccharomyces cerevisiae. Biochemistry. 2001 Sep 11;40(36):10800-9. PMID:11535055

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/1g2p"

@@ Line 1: / Line 1: @@
 ==CRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE==
-<StructureSection load='1g2p' size='340' side='right' caption='[[1g2p]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
+<StructureSection load='1g2p' size='340' side='right'caption='[[1g2p]], [[Resolution|resolution]] 1.75&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1g2p]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G2P OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1G2P FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1g2p]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G2P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G2P FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.75&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Adenine_phosphoribosyltransferase Adenine phosphoribosyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.4.2.7 2.4.2.7] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1g2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g2p OCA], [http://pdbe.org/1g2p PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1g2p RCSB], [http://www.ebi.ac.uk/pdbsum/1g2p PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1g2p ProSAT]</span></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=1g2p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g2p OCA], [https://pdbe.org/1g2p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g2p RCSB], [https://www.ebi.ac.uk/pdbsum/1g2p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g2p ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/APT1_YEAST APT1_YEAST]] Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.<ref>PMID:9864350</ref>
+[https://www.uniprot.org/uniprot/APT1_YEAST APT1_YEAST] Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis.<ref>PMID:9864350</ref>
 == 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/g2/1g2p_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/g2/1g2p_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 31: / Line 31: @@
 ==See Also==
-*[[Phosphoribosyltransferase|Phosphoribosyltransferase]]
+*[[Phosphoribosyltransferase 3D structures|Phosphoribosyltransferase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Adenine phosphoribosyltransferase]]
+[[Category: Large Structures]]
-[[Category: Almo, S C]]
+[[Category: Saccharomyces cerevisiae]]
-[[Category: Schramm, V L]]
+[[Category: Almo SC]]
-[[Category: Shi, W]]
+[[Category: Schramm VL]]
-[[Category: Tanaka, K S.E]]
+[[Category: Shi W]]
-[[Category: Catalytic loop]]
+[[Category: Tanaka KSE]]
-[[Category: Dimer]]
-[[Category: Transferase]]

1g2p

From Proteopedia

Current revision

CRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox