| Title | Crystal structure of D-serine deaminase from Burkholderia xenovorans LB400 (YP_556991.1) from BURKHOLDERIA XENOVORANS LB400 at 2.00 A resolution. | | Site | JCSG | | PDB Id | | Target Id | 381087 | | Molecular Characteristics | | Source | Burkholderia xenovorans lb400 | | Alias Ids | YP_556991.1 | Molecular Weight | 47105.53 Da. | | Residues | 425 | Isoelectric Point | 5.44 | | Sequence | mkvtnyqgatidpyskglgmvpgtsiqltdaarlewnllnedvslpaavlyadrvehnlkwmqafvaeyg vklaphgkttmapqlfrrqletgawgitlatahqvraayhggvsrvlmanqlvgrrnmmmvaellsdpe feffclvdsvegveqlgeffksvnkqlqvllelgvpggrtgvrdaaqrnavleaitrypdtlklagvel yegvlkeehevreflqsavavtrelveqerfarapavlsgagsawydvvaeefvkasetgkvevvlrpg cylthdvgiyrkaqtdifarnpvakkmgegllpalqlwayvqsipepdraiiglgkrdsafdagmpepa rhyrpgneaprdiaasegweifglmdqhaylripagadlkvgdmiafdishpcltfdkwrqvlvvdpay rvtevietff | | | BLAST FFAS |
| Structure Determination | | Method | XRAY | Chains | 2 | | Resolution (Å) | 2.00 | Rfree | 0.205 | | Matthews' coefficent | 2.46 | Rfactor | 0.163 | | Waters | 472 | Solvent Content | 50.10 |
| Ligand Information | | Ligands | GOL (GLYCEROL) x 4 | | Metals | NA (SODIUM) x 1 | |  | /content/body/table/tbody/tr/td[2]/center/table/tbody/tr[2]/td/center/span, reference to undefined name 'jmol': line 1, column 1 (click for details)MindTouch.Deki.Script.DekiScriptUndefinedNameException: reference to undefined name 'jmol': line 1, column 1
at MindTouch.Deki.Script.DekiScriptVar.Evaluate (MindTouch.Deki.Script.DekiScriptEnv env) [0x00000]
at MindTouch.Deki.Script.DekiScriptAccess.Evaluate (MindTouch.Deki.Script.DekiScriptEnv env, Boolean evaluateProperties) [0x00000]
at MindTouch.Deki.Script.DekiScriptAccess.Evaluate (MindTouch.Deki.Script.DekiScriptEnv env) [0x00000]
at MindTouch.Deki.Script.DekiScriptCall.Evaluate (MindTouch.Deki.Script.DekiScriptEnv env) [0x00000]
at MindTouch.Deki.Script.Dom.DekiScriptDomExpr.Evaluate (MindTouch.Deki.Script.DekiScriptEvalContext context, System.Xml.XmlNode parent, MindTouch.Deki.Script.DekiScriptEnv env) [0x00000] | |
| /content/body/table/tbody/tr/td[2]/center/table/tbody/tr[6]/td/center/table/tbody/tr/td/span, function 'template' failed (click for details)MindTouch.Deki.Script.DekiScriptInvokeException: function 'template' failed ---> System.ArgumentException: could not convert parameter 'target' (index 2) from list to str
at MindTouch.Deki.DekiScriptFunction+DekiScriptInvokeDelegateWrapper.Invoke (MindTouch.Deki.Script.DekiScriptLiteral arguments) [0x00000]
at MindTouch.Deki.DekiExtNativeFunction.Invoke (MindTouch.Deki.Script.DekiScriptLiteral arguments) [0x00000]
at MindTouch.Deki.Script.DekiScriptRuntime+<Invoke>d__0.MoveNext () [0x00000]
--- End of inner exception stack trace ---
at MindTouch.Deki.Script.DekiScriptRuntime+<Invoke>d__0.MoveNext () [0x00000]
at MindTouch.Tasking.Coroutine.Invoke (System.Func`1 invocation) [0x00000]
--- End of exception stack trace ---
at MindTouch.Deki.Script.DekiScriptRuntime.Invoke(XUri uri, DekiScriptLiteral args, DekiScriptEnv env, Result`1 result)
at MindTouch.Deki.Script.DekiScriptRuntime.Invoke(XUri uri, DekiScriptLiteral args, DekiScriptEnv env, Result`1 result)
at MindTouch.Deki.DekiWikiService.GetPageContents(DreamContext context, DreamMessage request, Result`1 response)
--- End of coroutine stack trace --- | | |
Protein Summary
381087 is a member of PF01168, alanine racemase N-term domain. This protein is likely a bacterial homolog of the yeast D-serine dehydratase YGL196W (see reference below). The protein functions as a dimer. It contains a TIM fold at the middle part, the N-term is involved in dimerization, the C-term folds into a separate domain, also near the domain interface.
It is likely that this enzyme functions in D-amino acid metabolism, and binds PLP, based on gene neighborhood and the structure similarity of the middle section with 1xfc. However, the active sites differs significantly, except for Lys78 and Arg275. As a result, further analysis is needed to understand the function of this protein (eg does it really binds PLP, how?).
The closest structural matches by SSM include: 1njj, 3c5q, 2qgh. The active site in the TIM domain (near H76) bears similarity to 1njj, but is not highly conserved.
Need to try co-xtallization with PLP.
Figure 1 monomer
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Figure 2 dimer
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Biochem. J. (2008) 409, 399–406 (Printed in Great Britain) doi:10.1042/BJ20070642
Ligand Summary
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.png?size=webview "pu9913a-dimer (1).png")
.png?size=webview "pu9913a-monomer (1).png")