Alr (PA4930) is the biosynthetic alanine racemase of Pseudomonas aeruginosa, a 358-residue PLP-dependent enzyme of the alanine racemase family. It interconverts L- and D-alanine (EC 5.1.1.1) with similar Km (about 1.1 mM) and Vmax in both directions, using PLP bound as an internal aldimine to Lys34, and supplies the D-alanine needed for the D-Ala-D-Ala terminus of peptidoglycan precursors. It functions as a homodimer in dynamic equilibrium with the monomer. P. aeruginosa also has a second, catabolic alanine racemase, DadX (PA5302), which serves D-alanine catabolism; Alr complements E. coli D-alanine auxotrophs.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | TOO GENERAL | Summary: Root-level catalytic activity from InterPro2GO. Reason: Entailed by the accepted GO:0008784 alanine racemase activity. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from PTN000775508, seeded by E. coli DadX (P29012). Alanine racemases are soluble cytoplasmic PLP enzymes with no signal peptide or TM segment. Reason: Plausible cytosolic location for a soluble racemase; not tested for this protein and not part of the core function. Supporting Evidence: file:PSEAE/alr/alr-uniprot.txt Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis. {ECO:0000269|PubMed:10977898}. |
| GO:0008784 alanine racemase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the PTN000775508 IBD, with eight seeds: Alr itself (expected self-seed), DadX of P. aeruginosa (Q9HTQ2), E. coli Alr (P0A6B4) and DadX (P29012), M. tuberculosis Alr (P9WQA9), two Vibrio cholerae racemases and S. pombe SPCC965.08c. The IBD stands without the Alr seed and the term suits the clade. Reason: Core activity, experimentally established for this protein and conserved across the alanine racemase family. Supporting Evidence: PMID:10977898 The dadX(PA) and alr(PA) genes have been sequenced, overexpressed, and their activity was demonstrated by complementing d-alanine auxotrophs of Escherichia coli. file:PSEAE/alr/alr-uniprot.txt Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis. {ECO:0000269|PubMed:10977898}. |
| GO:0008784 alanine racemase activity | IDA PMID:20971724 Correlation between catalytic activity and monomer-dimer equ... | ACCEPT | Summary: PseudoCAP IDA and one of eight seeds of PTN000775508. The paper compared the oligomeric state and Vmax of seven biosynthetic and catabolic alanine racemases including the P. aeruginosa enzymes. Reason: Seed verdict SOUND. The abstract states that Vmax was related to dimerisation for the biosynthetic and catabolic enzymes studied, which requires racemase assays; independent purified-enzyme evidence for P. aeruginosa Alr is in PMID:10977898 and PMID:29964014. Supporting Evidence: PMID:20971724 We analysed oligomerization states of seven alanine racemases, biosynthetic and catabolic, from Escherichia coli, Salmonella typhimurium, Pseudomonas aeruginosa, P. putida and P. fluorescens PMID:20971724 In both biosynthetic and catabolic alanine racemases, association constants for dimerization were high for the enzymes with high V(max) values. PMID:10977898 Both gene products were purified to electrophoretic homogeneity, the enzymes were characterized biochemically |
| GO:0008784 alanine racemase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (HAMAP/UniRule, InterPro, RHEA:20249, EC 5.1.1.1). Reason: Same claim as the experimental rows. Supporting Evidence: file:PSEAE/alr/alr-uniprot.txt Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis. {ECO:0000269|PubMed:10977898}. |
| GO:0009252 peptidoglycan biosynthetic process | IEA GO_REF:0000041 | KEEP AS NON CORE | Summary: UniPathway mapping to peptidoglycan biosynthesis. Alr supplies D-alanine, the substrate of Ddl for the D-Ala-D-Ala dipeptide of the peptidoglycan precursor. Reason: Alr makes a precursor of peptidoglycan synthesis (D-alanine supply), a conventional pathway annotation; the step it performs is captured more precisely by GO:0030632 D-alanine biosynthetic process. Supporting Evidence: file:PSEAE/alr/alr-uniprot.txt Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis. {ECO:0000269|PubMed:10977898}. |
| GO:0030170 pyridoxal phosphate binding | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA from PTN000775508 (seeds E. coli Alr, M. tuberculosis Alr). Alanine racemases bind PLP as an internal aldimine with the catalytic lysine (Lys34 here, modified residue in UniProt). Reason: True cofactor binding, ancillary to the racemase activity. Supporting Evidence: file:PSEAE/alr/alr-uniprot.txt MOD_RES 34 |
| GO:0030170 pyridoxal phosphate binding | IEA GO_REF:0000104 | KEEP AS NON CORE | Summary: UniRule transfer of PLP binding. Reason: Same claim as the IBA row. Supporting Evidence: file:PSEAE/alr/alr-uniprot.txt MOD_RES 34 |
| GO:0030632 D-alanine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN001253738 (seeds E. coli Alr, M. tuberculosis Alr). Alr is the biosynthetic racemase that supplies D-alanine; it complements E. coli D-alanine auxotrophs. Reason: Alr catalyses the single step of D-alanine biosynthesis from L-alanine. Supporting Evidence: PMID:10977898 The dadX(PA) and alr(PA) genes have been sequenced, overexpressed, and their activity was demonstrated by complementing d-alanine auxotrophs of Escherichia coli. file:PSEAE/alr/alr-uniprot.txt Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis. {ECO:0000269|PubMed:10977898}. |
| GO:0030632 D-alanine biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA for D-alanine biosynthesis. Reason: Same claim as the IBA row. Supporting Evidence: file:PSEAE/alr/alr-uniprot.txt Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis. {ECO:0000269|PubMed:10977898}. |
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Experiment: Construct single and double alr/dadX deletions in PAO1 and test D-alanine auxotrophy and D-cycloserine susceptibility.
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