1q0z

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of aclacinomycin methylesterase (RdmC) with bound product analogue, 10-decarboxymethylaclacinomycin A (DcmA)

Structural highlights

1q0z is a 1 chain structure with sequence from Streptomyces purpurascens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.95Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RDMC_STREF Involved in the biosynthesis of the anthracycline aclacinomycin which is an aromatic polyketide antibiotic that exhibits high cytotoxicity and is widely applied in the chemotherapy of a variety of cancers. Catalyzes the removal of the methoxy group from the C-15 position of aclacinomycin T and A to yield 15-demethoxyaclacinomycin T and A, respectively.^[1] ^[2]

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

Aclacinomycin methylesterase (RdmC) is one of the tailoring enzymes that modify the aklavinone skeleton in the biosynthesis of anthracyclines in Streptomyces species. The crystal structures of this enzyme from Streptomyces purpurascens in complex with the product analogues 10-decarboxymethylaclacinomycin T and 10-decarboxymethylaclacinomycin A were determined to nominal resolutions of 1.45 and 1.95 A, respectively. RdmC is built up of two domains. The larger alpha/beta domain shows the common alpha/beta hydrolase fold, whereas the smaller domain is alpha-helical. The active site and substrate binding pocket are located at the interface between the two domains. Decarboxymethylaclacinomycin T and decarboxymethylaclacinomycin A bind close to the catalytic triad (Ser102-His276-Asp248) in a hydrophobic pocket, with the sugar moieties located at the surface of the enzyme. The binding of the ligands is dominated by hydrophobic interactions, and specificity appears to be controlled mainly by the shape of the binding pocket rather than through specific hydrogen bonds. Mechanistic key features consistent with the structure of complexes of RdmC with product analogues are Ser102 acting as nucleophile and transition state stabilization by an oxyanion hole formed by the backbone amides of residues Gly32 and Met103.

Crystal structure of aclacinomycin methylesterase with bound product analogues: implications for anthracycline recognition and mechanism.,Jansson A, Niemi J, Mantsala P, Schneider G J Biol Chem. 2003 Oct 3;278(40):39006-13. Epub 2003 Jul 23. PMID:12878604^[3]

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

References

↑ Wang Y, Niemi J, Airas K, Ylihonko K, Hakala J, Mantsala P. Modifications of aclacinomycin T by aclacinomycin methyl esterase (RdmC) and aclacinomycin-10-hydroxylase (RdmB) from Streptomyces purpurascens. Biochim Biophys Acta. 2000 Jul 14;1480(1-2):191-200. PMID:11004563
↑ Niemi J, Mantsala P. Nucleotide sequences and expression of genes from Streptomyces purpurascens that cause the production of new anthracyclines in Streptomyces galilaeus. J Bacteriol. 1995 May;177(10):2942-5. PMID:7751313
↑ Jansson A, Niemi J, Mantsala P, Schneider G. Crystal structure of aclacinomycin methylesterase with bound product analogues: implications for anthracycline recognition and mechanism. J Biol Chem. 2003 Oct 3;278(40):39006-13. Epub 2003 Jul 23. PMID:12878604 doi:10.1074/jbc.M304008200

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/1q0z"

@@ Line 1: / Line 1: @@
 ==Crystal structure of aclacinomycin methylesterase (RdmC) with bound product analogue, 10-decarboxymethylaclacinomycin A (DcmA)==
-<StructureSection load='1q0z' size='340' side='right' caption='[[1q0z]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
+<StructureSection load='1q0z' size='340' side='right'caption='[[1q0z]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1q0z]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_25489 Atcc 25489]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q0Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1q0z]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_purpurascens Streptomyces purpurascens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q0Z FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=AKA:10-DECARBOXYMETHYLACLACINOMYCIN+A+(DCMAA)'>AKA</scene>, <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]] 1.95&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1q0r|1q0r]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=AKA:10-DECARBOXYMETHYLACLACINOMYCIN+A+(DCMAA)'>AKA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rdmc ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1924 ATCC 25489])</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=1q0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0z OCA], [https://pdbe.org/1q0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q0z RCSB], [https://www.ebi.ac.uk/pdbsum/1q0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q0z ProSAT]</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=1q0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q0z OCA], [http://pdbe.org/1q0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q0z RCSB], [http://www.ebi.ac.uk/pdbsum/1q0z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1q0z ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/RDMC_STREF RDMC_STREF]] Involved in the biosynthesis of the anthracycline aclacinomycin which is an aromatic polyketide antibiotic that exhibits high cytotoxicity and is widely applied in the chemotherapy of a variety of cancers. Catalyzes the removal of the methoxy group from the C-15 position of aclacinomycin T and A to yield 15-demethoxyaclacinomycin T and A, respectively.<ref>PMID:11004563</ref> <ref>PMID:7751313</ref>
+[https://www.uniprot.org/uniprot/RDMC_STREF RDMC_STREF] Involved in the biosynthesis of the anthracycline aclacinomycin which is an aromatic polyketide antibiotic that exhibits high cytotoxicity and is widely applied in the chemotherapy of a variety of cancers. Catalyzes the removal of the methoxy group from the C-15 position of aclacinomycin T and A to yield 15-demethoxyaclacinomycin T and A, respectively.<ref>PMID:11004563</ref> <ref>PMID:7751313</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/q0/1q0z_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q0/1q0z_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 30: / Line 29: @@
 </div>
 <div class="pdbe-citations 1q0z" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Methylesterase 3D structures|Methylesterase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 25489]]
+[[Category: Large Structures]]
-[[Category: Jansson, A]]
+[[Category: Streptomyces purpurascens]]
-[[Category: Mantsala, P]]
+[[Category: Jansson A]]
-[[Category: Niemi, J]]
+[[Category: Mantsala P]]
-[[Category: SPINE, Structural Proteomics in Europe]]
+[[Category: Niemi J]]
-[[Category: Schneider, G]]
+[[Category: Schneider G]]
-[[Category: Anthracycline]]
-[[Category: Hydrolase]]
-[[Category: Methylesterase]]
-[[Category: Polyketide]]
-[[Category: Spine]]
-[[Category: Streptomyce]]
-[[Category: Structural genomic]]
-[[Category: Structural proteomics in europe]]
-[[Category: Tailoring enzyme]]

1q0z

From Proteopedia

Current revision

Crystal structure of aclacinomycin methylesterase (RdmC) with bound product analogue, 10-decarboxymethylaclacinomycin A (DcmA)

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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