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1byi

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STRUCTURE OF APO-DETHIOBIOTIN SYNTHASE AT 0.97 ANGSTROMS RESOLUTION

Structural highlights

1byi is a 1 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 0.97Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BIOD1_ECOLI Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring. Only CTP can partially replace ATP while diaminobiotin is only 37% as effective as 7,8-diaminopelargonic acid.^[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

The crystal structure of the 224-residue protein dethiobiotin synthetase from Escherichia coli has been refined using X-ray diffraction data at 0.97 A resolution at 100 K. The model, consisting of 4143 protein atoms including 1859 H atoms and 436 solvent sites, was refined to a final R factor of 11.6% for all reflections, and has an estimated mean standard uncertainty for the atomic positions of 0.022 A, derived from inversion of the blocked matrix. The structure was refined with a full anisotropic model for the atomic displacement parameters using SHELX97. Stereochemical restraints were applied throughout the refinement. In the last cycles, the planarity of the peptide bonds was not restrained, resulting in a mean omega value of 179.6 degrees. Analysis of the most anisotropic regions of the protein shows that they form four clusters of residues. Alternate conformations for the side chains of 15 residues and for the main-chain atoms of six residues from three loops were included in the model. An analysis of C-HcO hydrogen bonds shows that such interactions occur rather frequently in DTBS; in total, 16 such hydrogen bonds were found. In the central beta-sheet, 13 C-HcO bonds between carbonyl O and Calpha H atoms were found. Other interactions of this type involve main-chain-side-chain and side-chain-side-chain C-HcO bonds. The model includes 436 water sites, of which 233 molecules form the first hydration shell. Analysis of the protein-solvent interactions shows that about one third of the accessible surface of the enzyme is not covered by ordered solvent. No difference in propensity for ordered solvent close to hydrophilic or hydrophobic surface areas was found. The comparison of the 100 K structure with the structure of the enzyme determined at room temperature shows several regions with different conformation, including areas in the active site, suggesting that structural transitions can occur during flash freezing. This observation questions one of the basic assumptions in the analysis of enzymatic reaction mechanisms using cryocrystallography.

Structure of dethiobiotin synthetase at 0.97 A resolution.,Sandalova T, Schneider G, Kack H, Lindqvist Y Acta Crystallogr D Biol Crystallogr. 1999 Mar;55(Pt 3):610-24. PMID:10089457^[3]

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

References

↑ Eisenberg MA, Krell K. Synthesis of desthiobiotin from 7,8-diaminopelargonic acid in biotin auxotrophs of Escherichia coli K-12. J Bacteriol. 1969 Jun;98(3):1227-31. PMID:4892372
↑ Krell K, Eisenberg MA. The purification and properties of dethiobiotin synthetase. J Biol Chem. 1970 Dec 25;245(24):6558-66. PMID:4921568
↑ Sandalova T, Schneider G, Kack H, Lindqvist Y. Structure of dethiobiotin synthetase at 0.97 A resolution. Acta Crystallogr D Biol Crystallogr. 1999 Mar;55(Pt 3):610-24. PMID:10089457

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/1byi"

@@ Line 1: / Line 1: @@
 ==STRUCTURE OF APO-DETHIOBIOTIN SYNTHASE AT 0.97 ANGSTROMS RESOLUTION==
-<StructureSection load='1byi' size='340' side='right' caption='[[1byi]], [[Resolution|resolution]] 0.97&Aring;' scene=''>
+<StructureSection load='1byi' size='340' side='right'caption='[[1byi]], [[Resolution|resolution]] 0.97&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1byi]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BYI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BYI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1byi]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BYI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BYI 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/Dethiobiotin_synthase Dethiobiotin synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.3.3 6.3.3.3] </span></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]] 0.97&#8491;</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=1byi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1byi OCA], [http://pdbe.org/1byi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1byi RCSB], [http://www.ebi.ac.uk/pdbsum/1byi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1byi 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=1byi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1byi OCA], [https://pdbe.org/1byi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1byi RCSB], [https://www.ebi.ac.uk/pdbsum/1byi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1byi ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BIOD1_ECOLI BIOD1_ECOLI]] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring. Only CTP can partially replace ATP while diaminobiotin is only 37% as effective as 7,8-diaminopelargonic acid.<ref>PMID:4892372</ref> <ref>PMID:4921568</ref>
+[https://www.uniprot.org/uniprot/BIOD1_ECOLI BIOD1_ECOLI] Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring. Only CTP can partially replace ATP while diaminobiotin is only 37% as effective as 7,8-diaminopelargonic acid.<ref>PMID:4892372</ref> <ref>PMID:4921568</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/by/1byi_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/by/1byi_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 28: @@
 </div>
 <div class="pdbe-citations 1byi" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Dethiobiotin synthetase 3D structures|Dethiobiotin synthetase 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Dethiobiotin synthase]]
 [[Category: Escherichia coli]]
-[[Category: Kaeck, H]]
+[[Category: Large Structures]]
-[[Category: Lindqvist, Y]]
+[[Category: Kaeck H]]
-[[Category: Sandalova, T]]
+[[Category: Lindqvist Y]]
-[[Category: Schneider, G]]
+[[Category: Sandalova T]]
-[[Category: Biotin synthesis]]
+[[Category: Schneider G]]
-[[Category: Cyclo-ligase]]
-[[Category: Ligase]]

1byi

From Proteopedia

Current revision

STRUCTURE OF APO-DETHIOBIOTIN SYNTHASE AT 0.97 ANGSTROMS RESOLUTION

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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