3pte: Difference between revisions

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-[[Image:3pte.png|left|200px]]
-{{STRUCTURE_3pte|  PDB=3pte  |  SCENE=  }}
+==THE REFINED CRYSTALLOGRAPHIC STRUCTURE OF A DD-PEPTIDASE PENICILLIN-TARGET ENZYME AT 1.6 A RESOLUTION==
+<StructureSection load='3pte' size='340' side='right'caption='[[3pte]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3pte]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Strsr Strsr]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1pte 1pte]. The May 2002 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Penicillin-binding Proteins''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2002_5 10.2210/rcsb_pdb/mom_2002_5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PTE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3PTE FirstGlance]. <br>
+</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Serine-type_D-Ala-D-Ala_carboxypeptidase Serine-type D-Ala-D-Ala carboxypeptidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.16.4 3.4.16.4] </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=3pte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pte OCA], [http://pdbe.org/3pte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3pte RCSB], [http://www.ebi.ac.uk/pdbsum/3pte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3pte ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/DAC_STRSR DAC_STRSR]] Catalyzes distinct carboxypeptidation and transpeptidation reactions during the last stages of wall peptidoglycan synthesis. Mistaking a beta-lactam antibiotic molecule for a normal substrate (i.e. a D-alanyl-D-alanine-terminated peptide), it becomes immobilized in the form of a long-lived, serine-ester-linked acyl enzyme and thus behave as penicillin-binding protein (PBP).
+== 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/pt/3pte_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/main_output.php?pdb_ID=3pte ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The D-alanyl-D-alanine peptidase from Streptomyces sp. R61 is a 37,500 dalton exocellular enzyme that has served as a model for membrane-bound peptidases that are involved in bacterial cell wall biosynthesis. Inhibition of these enzymes by beta-lactam antibiotics ultimately leads to bacterial cell death. The X-ray crystal structure of the R61 D-alanyl-D-alanine peptidase has been solved using multiple isomorphous replacement, simulated annealing and least squares refinement. The space group and unit cell parameters are P2(1)2(1)2(1) with a = 51.1 A, b = 67.3 A and c = 102.4 A. The structure has been refined using 2 sigma data to 1.6 A resolution with a crystallographic R-factor of 0.148. The model contains 347 residues (2938 atoms) and 254 solvent molecules. The overall temperature factor is 9.6 A2, and the estimated coordinate error is 0.14 A. The protein consists of a single polypeptide chain organized into two regions. One region contains a nine-stranded antiparallel beta-sheet with helices on both faces; this region includes both the amino and carboxyl termini. The second region is all helical. Sixty percent of the residues occur in helices or beta-sheet. The reactive Ser62 is found between the two regions of the enzyme at the amino end of the protein's longest-helix which begins with one turn of 3(10) helix and continues with four turns of alpha-helix. The active site is an elongated pocket that contains four basic and four aromatic residues. An oxyanion hole is formed by Ser62 NH and Thr301 NH. The pocket also contains the few key residues that are conserved in all penicillin-binding proteins and beta-lactamases. Two of these residues, Lys65 and Tyr159, are among the 16 side-chains that take on multiple conformations in the R61 crystal structure. Three of the 12 proline rings adopt two conformations which we believe has not been previously reported. There is no anionic acid equivalent to the catalytic Glu166 found in Class A beta-lactamases. Two ordered water molecules (O507 and O644) are found buried in the active site and hydrogen-bonded to each other (2.6 A). O507 could potentially act as the hydrolytic water molecule for deacylation.
-===THE REFINED CRYSTALLOGRAPHIC STRUCTURE OF A DD-PEPTIDASE PENICILLIN-TARGET ENZYME AT 1.6 A RESOLUTION===
+The refined crystallographic structure of a DD-peptidase penicillin-target enzyme at 1.6 A resolution.,Kelly JA, Kuzin AP J Mol Biol. 1995 Nov 24;254(2):223-36. PMID:7490745<ref>PMID:7490745</ref>
-{{ABSTRACT_PUBMED_7490745}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3pte" style="background-color:#fffaf0;"></div>
-[[3pte]] is a 1 chain structure of [[Penicillin-binding protein]] with sequence from [http://en.wikipedia.org/wiki/Streptomyces_sp. Streptomyces sp.]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1pte 1pte]. The May 2002 RCSB PDB [http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Penicillin-binding Proteins''  by David S. Goodsell is [http://dx.doi.org/10.2210/rcsb_pdb/mom_2002_5 10.2210/rcsb_pdb/mom_2002_5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PTE OCA].
 ==See Also==
-*[[Penicillin-binding protein|Penicillin-binding protein]]
+*[[Carboxypeptidase 3D structures|Carboxypeptidase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:007490745</ref><ref group="xtra">PMID:011917145</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Penicillin-binding Proteins]]
 [[Category: RCSB PDB Molecule of the Month]]
 [[Category: Serine-type D-Ala-D-Ala carboxypeptidase]]
-[[Category: Streptomyces sp.]]
+[[Category: Strsr]]
-[[Category: Kelly, J A.]]
+[[Category: Kelly, J A]]
-[[Category: Kuzin, A P.]]
+[[Category: Kuzin, A P]]
 [[Category: Hydrolase]]
 [[Category: Transpeptidase]]