4d9n

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine

Structural highlights

4d9n is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.5Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DPAL_ECOLI Catalyzes the alpha,beta-elimination reaction of both L- and D-alpha,beta-diaminopropionate (DAP) to form pyruvate and ammonia. In vitro the D-isomer of serine is degraded to pyruvate, though very poorly; other amino acids (L-serine, D- and L-threonine, D- and L-beta-Cl-alanine) are not substrates. In vivo allows poor growth on L-DAP or a DL-DAP mixture but not on D-DAP alone, this may be due to a poor promoter. DL-DAP is toxic in the absence of this enzyme, it may inhibit enzymes involved in the synthesis of pyruvate and aspartate, as well as amino acids derived from them.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Pyridoxal 5'-phosphate (PLP)-dependent enzymes utilize the unique chemistry of a pyridine ring to carry out diverse reactions involving amino acids. Diaminopropionate (DAP) ammonia-lyase (DAPAL) is a prokaryotic PLP-dependent enzyme that catalyzes the degradation of d- and l-forms of DAP to pyruvate and ammonia. Here, we report the first crystal structure of DAPAL from Escherichia coli (EcDAPAL) in tetragonal and monoclinic forms at 2.0 and 2.2 A resolutions, respectively. Structures of EcDAPAL soaked with substrates were also determined. EcDAPAL has a typical fold type II PLP-dependent enzyme topology consisting of a large and a small domain with the active site at the interface of the two domains. The enzyme is a homodimer with a unique biological interface not observed earlier. Structure of the enzyme in the tetragonal form had PLP bound at the active site, whereas the monoclinic structure was in the apo-form. Analysis of the apo and holo structures revealed that the region around the active site undergoes transition from a disordered to ordered state and assumes a conformation suitable for catalysis only upon PLP binding. A novel disulfide was found to occur near a channel that is likely to regulate entry of ligands to the active site. EcDAPAL soaked with dl-DAP revealed density at the active site appropriate for the reaction intermediate aminoacrylate, which is consistent with the observation that EcDAPAL has low activity under crystallization conditions. Based on the analysis of the structure and results of site-directed mutagenesis, a two-base mechanism of catalysis involving Asp(120) and Lys(77) is suggested.

Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis.,Bisht S, Rajaram V, Bharath SR, Kalyani JN, Khan F, Rao AN, Savithri HS, Murthy MR J Biol Chem. 2012 Jun 8;287(24):20369-81. Epub 2012 Apr 13. PMID:22505717^[5]

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

References

↑ Uo T, Yoshimura T, Nishiyama T, Esaki N. Gene cloning, purification, and characterization of 2,3-diaminopropionate ammonia-lyase from Escherichia coli. Biosci Biotechnol Biochem. 2002 Dec;66(12):2639-44. PMID:12596860 doi:http://dx.doi.org/10.1271/bbb.66.2639
↑ Khan F, Jala VR, Rao NA, Savithri HS. Characterization of recombinant diaminopropionate ammonia-lyase from Escherichia coli and Salmonella typhimurium. Biochem Biophys Res Commun. 2003 Jul 11;306(4):1083-8. PMID:12821154
↑ Kalyani JN, Ramachandra N, Kachroo AH, Mahadevan S, Savithri HS. Functional analysis of the genes encoding diaminopropionate ammonia lyase in Escherichia coli and Salmonella enterica serovar Typhimurium. J Bacteriol. 2012 Oct;194(20):5604-12. Epub 2012 Aug 17. PMID:22904288 doi:http://dx.doi.org/10.1128/JB.01362-12
↑ Bisht S, Rajaram V, Bharath SR, Kalyani JN, Khan F, Rao AN, Savithri HS, Murthy MR. Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis. J Biol Chem. 2012 Jun 8;287(24):20369-81. Epub 2012 Apr 13. PMID:22505717 doi:10.1074/jbc.M112.351809
↑ Bisht S, Rajaram V, Bharath SR, Kalyani JN, Khan F, Rao AN, Savithri HS, Murthy MR. Crystal Structure of Escherichia coli Diaminopropionate Ammonia-lyase Reveals Mechanism of Enzyme Activation and Catalysis. J Biol Chem. 2012 Jun 8;287(24):20369-81. Epub 2012 Apr 13. PMID:22505717 doi:10.1074/jbc.M112.351809

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

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OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4d9n"

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[4d9n]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4D9N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4D9N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</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]] 2.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DSN:D-SERINE'>DSN</scene>, <scene name='pdbligand=LLP:(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC+ACID'>LLP</scene></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=4d9n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4d9n OCA], [https://pdbe.org/4d9n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4d9n RCSB], [https://www.ebi.ac.uk/pdbsum/4d9n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4d9n ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/DPAL_ECOLI DPAL_ECOLI]] Catalyzes the alpha,beta-elimination reaction of both L- and D-alpha,beta-diaminopropionate (DAP) to form pyruvate and ammonia. In vitro the D-isomer of serine is degraded to pyruvate, though very poorly; other amino acids (L-serine, D- and L-threonine, D- and L-beta-Cl-alanine) are not substrates. In vivo allows poor growth on L-DAP or a DL-DAP mixture but not on D-DAP alone, this may be due to a poor promoter. DL-DAP is toxic in the absence of this enzyme, it may inhibit enzymes involved in the synthesis of pyruvate and aspartate, as well as amino acids derived from them.<ref>PMID:12596860</ref> <ref>PMID:12821154</ref> <ref>PMID:22904288</ref> <ref>PMID:22505717</ref>
+[https://www.uniprot.org/uniprot/DPAL_ECOLI DPAL_ECOLI] Catalyzes the alpha,beta-elimination reaction of both L- and D-alpha,beta-diaminopropionate (DAP) to form pyruvate and ammonia. In vitro the D-isomer of serine is degraded to pyruvate, though very poorly; other amino acids (L-serine, D- and L-threonine, D- and L-beta-Cl-alanine) are not substrates. In vivo allows poor growth on L-DAP or a DL-DAP mixture but not on D-DAP alone, this may be due to a poor promoter. DL-DAP is toxic in the absence of this enzyme, it may inhibit enzymes involved in the synthesis of pyruvate and aspartate, as well as amino acids derived from them.<ref>PMID:12596860</ref> <ref>PMID:12821154</ref> <ref>PMID:22904288</ref> <ref>PMID:22505717</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==

4d9n

From Proteopedia

Current revision

Crystal structure of Diaminopropionate ammonia lyase from Escherichia coli in complex with D-serine

Structural highlights

Function

Publication Abstract from PubMed

References

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