alanine/ornithine racemase family PLP-dependent enzyme similar to Acetoanaerobium sticklandii ornithine racemase (OR), which catalyzes the conversion of L-ornithine to D-ornithine, and could also racemize basic amino acids such as lysine and arginine
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; This subfamily ...
1-333
2.34e-160
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
:
Pssm-ID: 143490 [Multi-domain] Cd Length: 353 Bit Score: 452.77 E-value: 2.34e-160
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; This subfamily ...
1-333
2.34e-160
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Pssm-ID: 143490 [Multi-domain] Cd Length: 353 Bit Score: 452.77 E-value: 2.34e-160
ornithine racemase Orr; This type of ornithine racemase occurs in an operon for anaerobic ...
3-332
9.45e-80
ornithine racemase Orr; This type of ornithine racemase occurs in an operon for anaerobic oxidative degradation of L-ornithine as occurs in strict anaerobes such as Clostridium sticklandii. The enzyme from C. sticklandii was shown to act on the basic amino acids ornithine, lysine, and arginine. Additional close homologs, outside the family defined by this HMM, likely have similar activity profiles, but occur in different genomic contexts and would not receive the gene symbol orr.
Pssm-ID: 468706 Cd Length: 351 Bit Score: 247.51 E-value: 9.45e-80
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; This subfamily ...
1-333
2.34e-160
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase-like 1; This subfamily is composed of uncharacterized bacterial proteins with similarity to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Pssm-ID: 143490 [Multi-domain] Cd Length: 353 Bit Score: 452.77 E-value: 2.34e-160
ornithine racemase Orr; This type of ornithine racemase occurs in an operon for anaerobic ...
3-332
9.45e-80
ornithine racemase Orr; This type of ornithine racemase occurs in an operon for anaerobic oxidative degradation of L-ornithine as occurs in strict anaerobes such as Clostridium sticklandii. The enzyme from C. sticklandii was shown to act on the basic amino acids ornithine, lysine, and arginine. Additional close homologs, outside the family defined by this HMM, likely have similar activity profiles, but occur in different genomic contexts and would not receive the gene symbol orr.
Pssm-ID: 468706 Cd Length: 351 Bit Score: 247.51 E-value: 9.45e-80
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; This family includes ...
1-308
3.42e-09
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Alanine Racemase; This family includes predominantly bacterial alanine racemases (AR), some serine racemases (SerRac), and putative bifunctional enzymes containing N-terminal UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase (murF) and C-terminal AR domains. These proteins are fold type III PLP-dependent enzymes that play essential roles in peptidoglycan biosynthesis. AR catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. SerRac converts L-serine into its D-enantiomer (D-serine) for peptidoglycan synthesis. murF catalyzes the addition of D-Ala-D-Ala to UDPMurNAc-tripeptide, the final step in the synthesis of the cytoplasmic precursor of bacterial cell wall peptidoglycan. Members of this family contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. AR and other members of this family require dimer formation and the presence of the PLP cofactor for catalytic activity. Fungal ARs and eukaryotic serine racemases, which are fold types I and II PLP-dependent enzymes respectively, are excluded from this family.
Pssm-ID: 143481 [Multi-domain] Cd Length: 367 Bit Score: 57.51 E-value: 3.42e-09
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme ...
11-216
4.09e-09
Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes; The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these proteins may possess only limited D- to L-alanine racemase activity or non-specific racemase activity.
Pssm-ID: 143484 [Multi-domain] Cd Length: 211 Bit Score: 55.79 E-value: 4.09e-09
Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01
References:
Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
of the residues that compose this conserved feature have been mapped to the query sequence.
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