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Conserved domains on  [gi|1412671048|emb|SPZ75220|]
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D-serine dehydratase [Shigella boydii]

Protein Classification

PALP domain-containing protein( domain architecture ID 751)

PALP domain-containing protein belonging to the tryptophan synthase beta superfamily (fold type II) that consists of pyridoxal phosphate (PLP)-dependent enzymes that catalyze beta-replacement and beta-elimination reactions

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DsdA super family cl42541
D-serine dehydratase [Amino acid transport and metabolism];
1-147 1.53e-113

D-serine dehydratase [Amino acid transport and metabolism];


The actual alignment was detected with superfamily member COG3048:

Pssm-ID: 442282  Cd Length: 446  Bit Score: 330.23  E-value: 1.53e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKA 80
Cdd:COG3048   178 MSAALGFQVTVHMSADAKQWKKDLLRSKGVTVVEYEGDYSVAVEQGRKQAEADPNCHFVDDENSRDLFLGYAVAALRLKK 257

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1412671048  81 QFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQI 147
Cdd:COG3048   258 QLAEAGIVVDAEHPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGLATGLHDKI 324
 
Name Accession Description Interval E-value
DsdA COG3048
D-serine dehydratase [Amino acid transport and metabolism];
1-147 1.53e-113

D-serine dehydratase [Amino acid transport and metabolism];


Pssm-ID: 442282  Cd Length: 446  Bit Score: 330.23  E-value: 1.53e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKA 80
Cdd:COG3048   178 MSAALGFQVTVHMSADAKQWKKDLLRSKGVTVVEYEGDYSVAVEQGRKQAEADPNCHFVDDENSRDLFLGYAVAALRLKK 257

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1412671048  81 QFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQI 147
Cdd:COG3048   258 QLAEAGIVVDAEHPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGLATGLHDKI 324
PRK02991 PRK02991
D-serine dehydratase; Provisional
 1-147 7.90e-112

D-serine dehydratase; Provisional


Pssm-ID: 235096  Cd Length: 441  Bit Score: 325.69  E-value: 7.90e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKA 80
Cdd:PRK02991  175 MSAALGFKVTVHMSADARQWKKDKLRSHGVTVVEYEGDYGVAVEEGRKAAESDPNCYFIDDENSRTLFLGYAVAGLRLKA 254

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1412671048  81 QFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQI 147
Cdd:PRK02991  255 QLAEQGIVVDADHPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGLMTGLHDQI 321
D-Ser-dehyd cd06447
D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the ...
 1-147 5.28e-99

D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine to pyruvate and ammonia. D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive antagonist of beta-alanine in the biosynthetic pathway to pentothenate and coenzyme A. D-serine dehydratase is different from other pyridoxal-5'-phosphate-dependent enzymes in that it catalyzes alpha, beta-elimination reactions on amino acids.


Pssm-ID: 107208  Cd Length: 404  Bit Score: 291.56  E-value: 5.28e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKA 80
Cdd:cd06447   152 MAAALGFKVTVHMSADAKQWKKDKLRSKGVTVVEYETDYSKAVEEGRKQAAADPMCYFVDDENSRDLFLGYAVAASRLKA 231

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1412671048  81 QFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQI 147
Cdd:cd06447   232 QLAELGIKVDAEHPLFVYLPCGVGGAPGGVAFGLKLIFGDNVHCFFAEPTHSPCMLLGMATGLHDKI 298
D_Ser_am_lyase TIGR02035
D-serine ammonia-lyase; This family consists of D-serine ammonia-lyase (EC 4.3.1.18), a ...
 1-147 6.78e-99

D-serine ammonia-lyase; This family consists of D-serine ammonia-lyase (EC 4.3.1.18), a pyridoxal-phosphate enzyme that converts D-serine to pyruvate and NH3. This enzyme is also called D-serine dehydratase and D-serine deaminase and was previously designated EC 4.2.1.14. It is homologous to an enzyme that acts on threonine and may itself act weakly on threonine. [Energy metabolism, Amino acids and amines]


Pssm-ID: 211710  Cd Length: 431  Bit Score: 292.52  E-value: 6.78e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKA 80
Cdd:TIGR02035 170 ISAALGFQVTVHMSADARQWKKDKLRSHGVTVVEYESDYGVAVEEGRKAAQSDPNCYFIDDENSRTLFLGYAVAASRLKA 249

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1412671048  81 QFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQI 147
Cdd:TIGR02035 250 QFDQQGIIVDAEHPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVYTGLHEQI 316
PALP pfam00291
Pyridoxal-phosphate dependent enzyme; Members of this family are all pyridoxal-phosphate ...
 1-142 3.91e-18

Pyridoxal-phosphate dependent enzyme; Members of this family are all pyridoxal-phosphate dependent enzymes. This family includes: serine dehydratase EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16, tryptophan synthase beta chain EC:4.2.1.20, threonine synthase EC:4.2.99.2, cysteine synthase EC:4.2.99.8 P11096, cystathionine beta-synthase EC:4.2.1.22, 1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4.


Pssm-ID: 459749 [Multi-domain]  Cd Length: 295  Bit Score: 79.66  E-value: 3.91e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKa 80
Cdd:pfam00291  73 AAARLGLKVTIVVPEDAPPGKLLLMRALGAEVVLVGGDYDEAVAAARELAAEGPGAYYINQYDNPLNIEGYGTIGLEIL- 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1412671048  81 qfAQQGRIVDAdnplfVYLPCGVGGGPGGVAFGLKLAFGDhVHCFFAEPTHSPCMLLGVHTG 142
Cdd:pfam00291 152 --EQLGGDPDA-----VVVPVGGGGLIAGIARGLKELGPD-VRVIGVEPEGAPALARSLAAG 205
 
Name Accession Description Interval E-value
DsdA COG3048
D-serine dehydratase [Amino acid transport and metabolism];
1-147 1.53e-113

D-serine dehydratase [Amino acid transport and metabolism];


Pssm-ID: 442282  Cd Length: 446  Bit Score: 330.23  E-value: 1.53e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKA 80
Cdd:COG3048   178 MSAALGFQVTVHMSADAKQWKKDLLRSKGVTVVEYEGDYSVAVEQGRKQAEADPNCHFVDDENSRDLFLGYAVAALRLKK 257

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1412671048  81 QFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQI 147
Cdd:COG3048   258 QLAEAGIVVDAEHPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGLATGLHDKI 324
PRK02991 PRK02991
D-serine dehydratase; Provisional
 1-147 7.90e-112

D-serine dehydratase; Provisional


Pssm-ID: 235096  Cd Length: 441  Bit Score: 325.69  E-value: 7.90e-112
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKA 80
Cdd:PRK02991  175 MSAALGFKVTVHMSADARQWKKDKLRSHGVTVVEYEGDYGVAVEEGRKAAESDPNCYFIDDENSRTLFLGYAVAGLRLKA 254

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1412671048  81 QFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQI 147
Cdd:PRK02991  255 QLAEQGIVVDADHPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGLMTGLHDQI 321
D-Ser-dehyd cd06447
D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the ...
 1-147 5.28e-99

D-Serine dehydratase is a pyridoxal phosphate (PLP)-dependent enzyme which catalyzes the conversion of L- or D-serine to pyruvate and ammonia. D-serine dehydratase serves as a detoxifying enzyme in most E. coli strains where D-serine is a competitive antagonist of beta-alanine in the biosynthetic pathway to pentothenate and coenzyme A. D-serine dehydratase is different from other pyridoxal-5'-phosphate-dependent enzymes in that it catalyzes alpha, beta-elimination reactions on amino acids.


Pssm-ID: 107208  Cd Length: 404  Bit Score: 291.56  E-value: 5.28e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKA 80
Cdd:cd06447   152 MAAALGFKVTVHMSADAKQWKKDKLRSKGVTVVEYETDYSKAVEEGRKQAAADPMCYFVDDENSRDLFLGYAVAASRLKA 231

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1412671048  81 QFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQI 147
Cdd:cd06447   232 QLAELGIKVDAEHPLFVYLPCGVGGAPGGVAFGLKLIFGDNVHCFFAEPTHSPCMLLGMATGLHDKI 298
D_Ser_am_lyase TIGR02035
D-serine ammonia-lyase; This family consists of D-serine ammonia-lyase (EC 4.3.1.18), a ...
 1-147 6.78e-99

D-serine ammonia-lyase; This family consists of D-serine ammonia-lyase (EC 4.3.1.18), a pyridoxal-phosphate enzyme that converts D-serine to pyruvate and NH3. This enzyme is also called D-serine dehydratase and D-serine deaminase and was previously designated EC 4.2.1.14. It is homologous to an enzyme that acts on threonine and may itself act weakly on threonine. [Energy metabolism, Amino acids and amines]


Pssm-ID: 211710  Cd Length: 431  Bit Score: 292.52  E-value: 6.78e-99
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKA 80
Cdd:TIGR02035 170 ISAALGFQVTVHMSADARQWKKDKLRSHGVTVVEYESDYGVAVEEGRKAAQSDPNCYFIDDENSRTLFLGYAVAASRLKA 249

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1412671048  81 QFAQQGRIVDADNPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVHTGLHDQI 147
Cdd:TIGR02035 250 QFDQQGIIVDAEHPLFVYLPCGVGGGPGGVAFGLKLAFGDHVHCFFAEPTHSPCMLLGVYTGLHEQI 316
Trp-synth-beta_II cd00640
Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP) ...
 1-101 1.96e-18

Tryptophan synthase beta superfamily (fold type II); this family of pyridoxal phosphate (PLP)-dependent enzymes catalyzes beta-replacement and beta-elimination reactions. This CD corresponds to aminocyclopropane-1-carboxylate deaminase (ACCD), tryptophan synthase beta chain (Trp-synth_B), cystathionine beta-synthase (CBS), O-acetylserine sulfhydrylase (CS), serine dehydratase (Ser-dehyd), threonine dehydratase (Thr-dehyd), diaminopropionate ammonia lyase (DAL), and threonine synthase (Thr-synth). ACCD catalyzes the conversion of 1-aminocyclopropane-1-carboxylate to alpha-ketobutyrate and ammonia. Tryptophan synthase folds into a tetramer, where the beta chain is the catalytic PLP-binding subunit and catalyzes the formation of L-tryptophan from indole and L-serine. CBS is a tetrameric hemeprotein that catalyzes condensation of serine and homocysteine to cystathionine. CS is a homodimer that catalyzes the formation of L-cysteine from O-acetyl-L-serine. Ser-dehyd catalyzes the conversion of L- or D-serine to pyruvate and ammonia. Thr-dehyd is active as a homodimer and catalyzes the conversion of L-threonine to 2-oxobutanoate and ammonia. DAL is also a homodimer and catalyzes the alpha, beta-elimination reaction of both L- and D-alpha, beta-diaminopropionate to form pyruvate and ammonia. Thr-synth catalyzes the formation of threonine and inorganic phosphate from O-phosphohomoserine.


Pssm-ID: 107202 [Multi-domain]  Cd Length: 244  Bit Score: 79.48  E-value: 1.96e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKA 80
Cdd:cd00640    68 AAARLGLKCTIVMPEGASPEKVAQMRALGAEVVLVPGDFDDAIALAKELAEEDPGAYYVNQFDNPANIAGQGTIGLEILE 147

                          90       100
                  ....*....|....*....|.
gi 1412671048  81 QFAQQgrivdadNPLFVYLPC 101
Cdd:cd00640   148 QLGGQ-------KPDAVVVPV 161
PALP pfam00291
Pyridoxal-phosphate dependent enzyme; Members of this family are all pyridoxal-phosphate ...
 1-142 3.91e-18

Pyridoxal-phosphate dependent enzyme; Members of this family are all pyridoxal-phosphate dependent enzymes. This family includes: serine dehydratase EC:4.2.1.13 P20132, threonine dehydratase EC:4.2.1.16, tryptophan synthase beta chain EC:4.2.1.20, threonine synthase EC:4.2.99.2, cysteine synthase EC:4.2.99.8 P11096, cystathionine beta-synthase EC:4.2.1.22, 1-aminocyclopropane-1-carboxylate deaminase EC:4.1.99.4.


Pssm-ID: 459749 [Multi-domain]  Cd Length: 295  Bit Score: 79.66  E-value: 3.91e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   1 MSARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDPNCFFIDDENSRTLFLGYSVAGQRLKa 80
Cdd:pfam00291  73 AAARLGLKVTIVVPEDAPPGKLLLMRALGAEVVLVGGDYDEAVAAARELAAEGPGAYYINQYDNPLNIEGYGTIGLEIL- 151

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1412671048  81 qfAQQGRIVDAdnplfVYLPCGVGGGPGGVAFGLKLAFGDhVHCFFAEPTHSPCMLLGVHTG 142
Cdd:pfam00291 152 --EQLGGDPDA-----VVVPVGGGGLIAGIARGLKELGPD-VRVIGVEPEGAPALARSLAAG 205
Thr-synth_1 cd01563
Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last ...
 2-76 1.26e-03

Threonine synthase is a pyridoxal phosphate (PLP) dependent enzyme that catalyses the last reaction in the synthesis of threonine from aspartate. It proceeds by converting O-phospho-L-homoserine (OPH) into threonine and inorganic phosphate. In plants, OPH is an intermediate between the methionine and threonine/isoleucine pathways. Thus threonine synthase competes for OPH with cystathionine-gamma-synthase, the first enzyme in the methionine pathway. These enzymes are in general dimers. Members of this CD, Thr-synth_1, are widely distributed in bacteria, archaea and higher plants.


Pssm-ID: 107206 [Multi-domain]  Cd Length: 324  Bit Score: 38.34  E-value: 1.26e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1412671048   2 SARIGFKVTVHMSADARAWKKAKLRSHGVTVVEYEQDYGVAVEEGRKAAQSDP-------NCFFIddENSRTlfLGYSVA 74
Cdd:cd01563    89 AARAGIKCVVFLPAGKALGKLAQALAYGATVLAVEGNFDDALRLVRELAEENWiylsnslNPYRL--EGQKT--IAFEIA 164


                  ..
gi 1412671048  75 GQ 76
Cdd:cd01563   165 EQ 166
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options: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.
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