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1n7k

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Revision as of 09:21, 29 September 2021

Unique tetrameric structure of deoxyribose phosphate aldolase from Aeropyrum pernix

Structural highlights

1n7k is a 2 chain structure with sequence from Aerpx. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Activity:	Deoxyribose-phosphate aldolase, with EC number 4.1.2.4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

[DEOC_AERPE] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.^[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

A gene encoding a 2-deoxy-d-ribose-5-phosphate aldolase (DERA) homolog was identified in the hyperthermophilic Archaea Aeropyrum pernix. The gene was overexpressed in Escherichia coli, and the produced enzyme was purified and characterized. The enzyme is an extremely thermostable DERA; its activity was not lost after incubation at 100 degrees C for 10 min. The enzyme has a molecular mass of approximately 93 kDa and consists of four subunits with an identical molecular mass of 24 kDa. This is the first report of the presence of tetrameric DERA. The three-dimensional structure of the enzyme was determined by x-ray analysis. The subunit folds into an alpha/beta-barrel. The asymmetric unit consists of two homologous subunits, and a crystallographic 2-fold axis generates the functional tetramer. The main chain coordinate of the monomer of the A. pernix enzyme is quite similar to that of the E. coli enzyme. There was no significant difference in hydrophobic interactions and the number of ion pairs between the monomeric structures of the two enzymes. However, a significant difference in the quaternary structure was observed. The area of the subunit-subunit interface in the dimer of the A. pernix enzyme is much larger compared with the E. coli enzyme. In addition, the A. pernix enzyme is 10 amino acids longer than the E. coli enzyme in the N-terminal region and has an additional N-terminal helix. The N-terminal helix produces a unique dimer-dimer interface. This promotes the formation of a functional tetramer of the A. pernix enzyme and strengthens the hydrophobic intersubunit interactions. These structural features are considered to be responsible for the extremely high stability of the A. pernix enzyme. This is the first description of the structure of hyperthermophilic DERA and of aldolase from the Archaea domain.

The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix.,Sakuraba H, Tsuge H, Shimoya I, Kawakami R, Goda S, Kawarabayasi Y, Katunuma N, Ago H, Miyano M, Ohshima T J Biol Chem. 2003 Mar 21;278(12):10799-806. Epub 2003 Jan 15. PMID:12529358^[2]

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

References

↑ Sakuraba H, Tsuge H, Shimoya I, Kawakami R, Goda S, Kawarabayasi Y, Katunuma N, Ago H, Miyano M, Ohshima T. The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix. J Biol Chem. 2003 Mar 21;278(12):10799-806. Epub 2003 Jan 15. PMID:12529358 doi:10.1074/jbc.M212449200
↑ Sakuraba H, Tsuge H, Shimoya I, Kawakami R, Goda S, Kawarabayasi Y, Katunuma N, Ago H, Miyano M, Ohshima T. The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix. J Biol Chem. 2003 Mar 21;278(12):10799-806. Epub 2003 Jan 15. PMID:12529358 doi:10.1074/jbc.M212449200

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/1n7k"

@@ Line 3: / Line 3: @@
 <StructureSection load='1n7k' size='340' side='right'caption='[[1n7k]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1n7k]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N7K FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1n7k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerpx Aerpx]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N7K 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/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] </span></td></tr>
+</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribose-phosphate_aldolase Deoxyribose-phosphate aldolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.2.4 4.1.2.4] </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=1n7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7k OCA], [http://pdbe.org/1n7k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n7k RCSB], [http://www.ebi.ac.uk/pdbsum/1n7k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n7k ProSAT], [http://www.topsan.org/Proteins/RSGI/1n7k TOPSAN]</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=1n7k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7k OCA], [https://pdbe.org/1n7k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n7k RCSB], [https://www.ebi.ac.uk/pdbsum/1n7k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n7k ProSAT], [https://www.topsan.org/Proteins/RSGI/1n7k TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/DEOC_AERPE DEOC_AERPE]] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.<ref>PMID:12529358</ref>
+[[https://www.uniprot.org/uniprot/DEOC_AERPE DEOC_AERPE]] Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.<ref>PMID:12529358</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]

1n7k

From Proteopedia

Revision as of 09:21, 29 September 2021

Unique tetrameric structure of deoxyribose phosphate aldolase from Aeropyrum pernix

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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