1l6f

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Alanine racemase bound with N-(5'-phosphopyridoxyl)-L-alanine

Structural highlights

1l6f is a 2 chain structure with sequence from Atcc 12980. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:PP3
NonStd Res:KCX
Activity:Alanine racemase, with EC number 5.1.1.1
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[ALR_GEOSE] Catalyzes the interconversion of L-alanine and D-alanine. Also weakly active on serine.[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 structures of alanine racemase bound with reaction intermediate analogs, N-(5'-phosphopyridoxyl)-L-alanine (PLP-L-Ala) and N-(5'-phosphopyridoxyl)-D-alanine (PLP-D-Ala), were determined at 2.0-A resolution with the crystallographic R factor of 17.2 for PLP-L-Ala and 16.9 for PLP-D-Ala complexes. They were quite similar not only to each other but also to the structure of the native pyridoxal 5'-phosphate (PLP)-form enzyme; root mean square deviations at Calpha among the three structures were less than 0.28 A. The side chains of the amino acid residues around the PLP-L-Ala and PLP-D-Ala were virtually superimposable on each other as well as on those around PLP of the native holoenzyme. The alpha-hydrogen of the alanine moiety of PLP-L-Ala was located near the OH of Tyr(265)', whereas that of PLP-D-Ala was near the NZ of Lys(39). These support the previous findings that Tyr(265)' and Lys(39) are the catalytic bases removing alpha-hydrogen from L- and D-alanine, respectively. The prerequisite for this two-base mechanism is that the alpha-proton abstracted from the substrate is transferred (directly or indirectly) between the NZ of Lys(39) and the OH of Tyr(265'); otherwise the enzyme reaction stops after a single turnover. Only the carboxylate oxygen atom of either PLP-Ala enantiomer occurred at a reasonable position that can mediate the proton transfer; neither the amino acid side chains nor the water molecules were located in the vicinity. Therefore, we propose a mechanism of alanine racemase reaction in which the substrate carboxyl group directly participates in the catalysis by mediating the proton transfer between the two catalytic bases, Lys(39) and Tyr(265)'. The results of molecular orbital calculation also support this mechanism.

Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine.,Watanabe A, Yoshimura T, Mikami B, Hayashi H, Kagamiyama H, Esaki N J Biol Chem. 2002 May 24;277(21):19166-72. Epub 2002 Mar 8. PMID:11886871[3]

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

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See Also

References

  1. Watanabe A, Yoshimura T, Mikami B, Esaki N. Tyrosine 265 of alanine racemase serves as a base abstracting alpha-hydrogen from L-alanine: the counterpart residue to lysine 39 specific to D-alanine. J Biochem. 1999 Oct;126(4):781-6. PMID:10502689
  2. Patrick WM, Weisner J, Blackburn JM. Site-directed mutagenesis of Tyr354 in Geobacillus stearothermophilus alanine racemase identifies a role in controlling substrate specificity and a possible role in the evolution of antibiotic resistance. Chembiochem. 2002 Aug 2;3(8):789-92. PMID:12203980 doi:<789::AID-CBIC789>3.0.CO;2-D http://dx.doi.org/10.1002/1439-7633(20020802)3:8<789::AID-CBIC789>3.0.CO;2-D
  3. Watanabe A, Yoshimura T, Mikami B, Hayashi H, Kagamiyama H, Esaki N. Reaction mechanism of alanine racemase from Bacillus stearothermophilus: x-ray crystallographic studies of the enzyme bound with N-(5'-phosphopyridoxyl)alanine. J Biol Chem. 2002 May 24;277(21):19166-72. Epub 2002 Mar 8. PMID:11886871 doi:10.1074/jbc.M201615200

Contents


1l6f, resolution 2.00Å

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