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Conserved domains on  [gi|15242275|ref|NP_200023|]
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Dihydrodipicolinate reductase, bacterial/plant [Arabidopsis thaliana]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
DapB super family cl43090
4-hydroxy-tetrahydrodipicolinate reductase [Amino acid transport and metabolism]; ...
 34-298 5.69e-35

4-hydroxy-tetrahydrodipicolinate reductase [Amino acid transport and metabolism]; 4-hydroxy-tetrahydrodipicolinate reductase is part of the Pathway/BioSystem: Lysine biosynthesis


The actual alignment was detected with superfamily member COG0289:

Pssm-ID: 440058 [Multi-domain]  Cd Length: 257  Bit Score: 126.77  E-value: 5.69e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275  34 IKVIINGAAKEIGRAAVVAVTKARGMELAGAVD-NHFVGEDIGLLCdmeepLEIPVVSDLTMVLgsisqgKEVGVVIDFT 112
Cdd:COG0289   1 IKIAVAGASGRMGRELIRAVLEAPDLELVAAIDrPGSPGQDAGELA-----LGVPVTDDLEEAL------AKADVVIDFT 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275 113 DPSTVYENVKQATAFGmKSVVyvprI-----KPETVSALSALCDKAtmGCLVAPTLSIGSILLQQAVIMASFHYNN---V 184
Cdd:COG0289  70 HPEATLENLEAALEAG-VPVV----IgttgfSEEQLAELEEAAKGI--PVLIAPNFSLGVNLLFKLAEEAAKYLGDdydI 142

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275 185 ELVES-RPNAADLPSPEAIQIANNISNLGQIYNREDSSTDVQARGQVIGEDGVRVHSMVLPGLPSSTQVYFSSPGDVYTV 263
Cdd:COG0289 143 EIIEAhHRQKVDAPSGTALKLAEAIAEARGRDLDDVAVYGREGITGARKKGEIGIHSVRGGDIVGEHTVIFAGEGERIEI 222

                       250       260       270
                ....*....|....*....|....*....|....*
gi 15242275 264 KHDIIDVRSLMPGLLLAIRKVVRLKNLVYGLEKFL 298
Cdd:COG0289 223 RHDASSRESFAPGALLAARWLAGKPPGLYGMEDVL 257
 
Name Accession Description Interval E-value
DapB COG0289
4-hydroxy-tetrahydrodipicolinate reductase [Amino acid transport and metabolism]; ...
 34-298 5.69e-35

4-hydroxy-tetrahydrodipicolinate reductase [Amino acid transport and metabolism]; 4-hydroxy-tetrahydrodipicolinate reductase is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 440058 [Multi-domain]  Cd Length: 257  Bit Score: 126.77  E-value: 5.69e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275  34 IKVIINGAAKEIGRAAVVAVTKARGMELAGAVD-NHFVGEDIGLLCdmeepLEIPVVSDLTMVLgsisqgKEVGVVIDFT 112
Cdd:COG0289   1 IKIAVAGASGRMGRELIRAVLEAPDLELVAAIDrPGSPGQDAGELA-----LGVPVTDDLEEAL------AKADVVIDFT 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275 113 DPSTVYENVKQATAFGmKSVVyvprI-----KPETVSALSALCDKAtmGCLVAPTLSIGSILLQQAVIMASFHYNN---V 184
Cdd:COG0289  70 HPEATLENLEAALEAG-VPVV----IgttgfSEEQLAELEEAAKGI--PVLIAPNFSLGVNLLFKLAEEAAKYLGDdydI 142

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275 185 ELVES-RPNAADLPSPEAIQIANNISNLGQIYNREDSSTDVQARGQVIGEDGVRVHSMVLPGLPSSTQVYFSSPGDVYTV 263
Cdd:COG0289 143 EIIEAhHRQKVDAPSGTALKLAEAIAEARGRDLDDVAVYGREGITGARKKGEIGIHSVRGGDIVGEHTVIFAGEGERIEI 222

                       250       260       270
                ....*....|....*....|....*....|....*
gi 15242275 264 KHDIIDVRSLMPGLLLAIRKVVRLKNLVYGLEKFL 298
Cdd:COG0289 223 RHDASSRESFAPGALLAARWLAGKPPGLYGMEDVL 257
DapB_C pfam05173
Dihydrodipicolinate reductase, C-terminus; Dihydrodipicolinate reductase (DapB) reduces the ...
 172-298 4.30e-27

Dihydrodipicolinate reductase, C-terminus; Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain.


Pssm-ID: 461568  Cd Length: 122  Bit Score: 102.20  E-value: 4.30e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275   172 QAVIMASFHYNN---VELVESRPNA-ADLPSPEAIQIANNISNLGQIYNREDsstdvqargQVIGEDGVRVHSMVLPGLP 247
Cdd:pfam05173   1 KLAKEAAKLLGDaydVEIIESHHNQkKDAPSGTALKLAEAIAELGARKNKWA---------RGAARDGIGIHSVRGGGVV 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15242275   248 SSTQVYFSSPGDVYTVKHDIIDVRSLMPGLLLAIRKVVRLKNLVYGLEKFL 298
Cdd:pfam05173  72 GEHTVLFAGDGERIEITHDAHSREIFAPGALLAARWLAGKKPGLYGMEDVL 122
DHDPR_N cd02274
N-terminal NAD(P)-binding domain of dihydrodipicolinate reductase (DHDPR) and similar proteins; ...
 34-161 5.88e-14

N-terminal NAD(P)-binding domain of dihydrodipicolinate reductase (DHDPR) and similar proteins; DHDPR (EC 1.17.1.8), also called 4-hydroxy-tetrahydrodipicolinate reductase, or HTPA reductase, is a product of an essential gene referred to as dapB. It catalyzes the NAD(P)H-dependent reduction of 2,3-dihydrodipicolinate (DHDP) to 2,3,4,5-tetrahydrodipicolinate (THDP). DHDPR could also function as a dehydratase in addition to the role of a nucleotide dependent reductase. DHDPR is a component of the biosynthetic pathway that generates meso-diaminopimelate, a component of bacterial cell walls, and the amino acid L-lysine in various bacteria, archaea, cyanobacteria and higher plants. The enzyme is a homotetramer where each monomer is composed of two domains, an N-terminal NAD(P)-binding domain which forms a Rossmann fold, and a C-terminal substrate-binding domain that forms an open, mixed alpha-beta sandwich.


Pssm-ID: 467611 [Multi-domain]  Cd Length: 139  Bit Score: 67.58  E-value: 5.88e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275  34 IKVIINGAAKEIGRAAVVAVTKARGMELAGAVDNH---FVGEDIGLLCDMEepLEIPVVSDLTMVLgsisqgKEVGVVID 110
Cdd:cd02274   1 IKVAVAGATGRMGRELVKAILEAPDLELVGAVDRPgsgLLGGDAGGLAGIG--TGVIVSLDLELAA------ADADVVID 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 15242275 111 FTDPSTVYENVKQATAFGMKSVVYVPRIKPETVSALSALCDKatMGCLVAP 161
Cdd:cd02274  73 FTTPEATLENLEAAAKAGVPLVIGTTGFSEEQLAEIEEAAKK--IPVVIAP 121
 
Name Accession Description Interval E-value
DapB COG0289
4-hydroxy-tetrahydrodipicolinate reductase [Amino acid transport and metabolism]; ...
 34-298 5.69e-35

4-hydroxy-tetrahydrodipicolinate reductase [Amino acid transport and metabolism]; 4-hydroxy-tetrahydrodipicolinate reductase is part of the Pathway/BioSystem: Lysine biosynthesis


Pssm-ID: 440058 [Multi-domain]  Cd Length: 257  Bit Score: 126.77  E-value: 5.69e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275  34 IKVIINGAAKEIGRAAVVAVTKARGMELAGAVD-NHFVGEDIGLLCdmeepLEIPVVSDLTMVLgsisqgKEVGVVIDFT 112
Cdd:COG0289   1 IKIAVAGASGRMGRELIRAVLEAPDLELVAAIDrPGSPGQDAGELA-----LGVPVTDDLEEAL------AKADVVIDFT 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275 113 DPSTVYENVKQATAFGmKSVVyvprI-----KPETVSALSALCDKAtmGCLVAPTLSIGSILLQQAVIMASFHYNN---V 184
Cdd:COG0289  70 HPEATLENLEAALEAG-VPVV----IgttgfSEEQLAELEEAAKGI--PVLIAPNFSLGVNLLFKLAEEAAKYLGDdydI 142

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275 185 ELVES-RPNAADLPSPEAIQIANNISNLGQIYNREDSSTDVQARGQVIGEDGVRVHSMVLPGLPSSTQVYFSSPGDVYTV 263
Cdd:COG0289 143 EIIEAhHRQKVDAPSGTALKLAEAIAEARGRDLDDVAVYGREGITGARKKGEIGIHSVRGGDIVGEHTVIFAGEGERIEI 222

                       250       260       270
                ....*....|....*....|....*....|....*
gi 15242275 264 KHDIIDVRSLMPGLLLAIRKVVRLKNLVYGLEKFL 298
Cdd:COG0289 223 RHDASSRESFAPGALLAARWLAGKPPGLYGMEDVL 257
DapB_C pfam05173
Dihydrodipicolinate reductase, C-terminus; Dihydrodipicolinate reductase (DapB) reduces the ...
 172-298 4.30e-27

Dihydrodipicolinate reductase, C-terminus; Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The C-terminal domain of DapB has been proposed to be the substrate- binding domain.


Pssm-ID: 461568  Cd Length: 122  Bit Score: 102.20  E-value: 4.30e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275   172 QAVIMASFHYNN---VELVESRPNA-ADLPSPEAIQIANNISNLGQIYNREDsstdvqargQVIGEDGVRVHSMVLPGLP 247
Cdd:pfam05173   1 KLAKEAAKLLGDaydVEIIESHHNQkKDAPSGTALKLAEAIAELGARKNKWA---------RGAARDGIGIHSVRGGGVV 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15242275   248 SSTQVYFSSPGDVYTVKHDIIDVRSLMPGLLLAIRKVVRLKNLVYGLEKFL 298
Cdd:pfam05173  72 GEHTVLFAGDGERIEITHDAHSREIFAPGALLAARWLAGKKPGLYGMEDVL 122
DapB_N pfam01113
Dihydrodipicolinate reductase, N-terminus; Dihydrodipicolinate reductase (DapB) reduces the ...
 34-161 8.59e-18

Dihydrodipicolinate reductase, N-terminus; Dihydrodipicolinate reductase (DapB) reduces the alpha,beta-unsaturated cyclic imine, dihydro-dipicolinate. This reaction is the second committed step in the biosynthesis of L-lysine and its precursor meso-diaminopimelate, which are critical for both protein and cell wall biosynthesis. The N-terminal domain of DapB binds the dinucleotide NADPH.


Pssm-ID: 460069 [Multi-domain]  Cd Length: 121  Bit Score: 77.66  E-value: 8.59e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275    34 IKVIINGAAKEIGRAAVVAVTKARGMELAGAVD---NHFVGEDIGLLCdmeePLEIPVVSDLTMVLgsisqgKEVGVVID 110
Cdd:pfam01113   1 IKIAVAGASGRMGRELIKAVLEAPDLELVAAVDrpgSSLLGSDAGELA----PLGVPVTDDLEEVL------ADADVLID 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 15242275   111 FTDPSTVYENVKQATAFGMKSVVYVPRIKPETVSALSALCDKatMGCLVAP 161
Cdd:pfam01113  71 FTTPEATLENLEFALKHGVPLVIGTTGFTEEQLAELKEAAKK--IPIVIAP 119
DHDPR_N cd02274
N-terminal NAD(P)-binding domain of dihydrodipicolinate reductase (DHDPR) and similar proteins; ...
 34-161 5.88e-14

N-terminal NAD(P)-binding domain of dihydrodipicolinate reductase (DHDPR) and similar proteins; DHDPR (EC 1.17.1.8), also called 4-hydroxy-tetrahydrodipicolinate reductase, or HTPA reductase, is a product of an essential gene referred to as dapB. It catalyzes the NAD(P)H-dependent reduction of 2,3-dihydrodipicolinate (DHDP) to 2,3,4,5-tetrahydrodipicolinate (THDP). DHDPR could also function as a dehydratase in addition to the role of a nucleotide dependent reductase. DHDPR is a component of the biosynthetic pathway that generates meso-diaminopimelate, a component of bacterial cell walls, and the amino acid L-lysine in various bacteria, archaea, cyanobacteria and higher plants. The enzyme is a homotetramer where each monomer is composed of two domains, an N-terminal NAD(P)-binding domain which forms a Rossmann fold, and a C-terminal substrate-binding domain that forms an open, mixed alpha-beta sandwich.


Pssm-ID: 467611 [Multi-domain]  Cd Length: 139  Bit Score: 67.58  E-value: 5.88e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275  34 IKVIINGAAKEIGRAAVVAVTKARGMELAGAVDNH---FVGEDIGLLCDMEepLEIPVVSDLTMVLgsisqgKEVGVVID 110
Cdd:cd02274   1 IKVAVAGATGRMGRELVKAILEAPDLELVGAVDRPgsgLLGGDAGGLAGIG--TGVIVSLDLELAA------ADADVVID 72

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|.
gi 15242275 111 FTDPSTVYENVKQATAFGMKSVVYVPRIKPETVSALSALCDKatMGCLVAP 161
Cdd:cd02274  73 FTTPEATLENLEAAAKAGVPLVIGTTGFSEEQLAEIEEAAKK--IPVVIAP 121
nat-AmDH_N_like cd24146
N-terminal NAD(P)-binding domain of native NAD(P)H-dependent amine dehydrogenases (nat-AmDHs) ...
 34-159 4.40e-06

N-terminal NAD(P)-binding domain of native NAD(P)H-dependent amine dehydrogenases (nat-AmDHs) and similar proteins; The family corresponds to a group of native NAD(P)H-dependent amine dehydrogenases (nat-AmDHs) that catalyze the reductive amination of ketone and aldehyde substrates using NAD(P)H as the hydride source. nat-AmDHs can naturally catalyze the amination of 'neutral' carbonyl compounds using ammonia. They possess tremendous potential for the efficient asymmetric synthesis of alpha-chiral amines. The family also contains 2,4-diaminopentanoate dehydrogenase (DAPDH) and similar proteins. DAPDH, also known as ORD, is involved in the ornithine fermentation pathway. It catalyzes the oxidative deamination of (2R,4S)-2,4-diaminopentanoate ((2R,4S)-DAP) to yield 2-amino-4-ketopentanoate (AKP). Although DAPDH is more efficient with (2R,4S)-DAP, the diastereoisomer (2R,4R)-DAP can also be metabolized. Different forms of DAPDH exist which utilize NAD(+) (EC 1.4.1.26) or NAD(+)/NADP(+) (EC 1.4.1.12). Members of this family contain an N-terminal Rossmann fold NAD(P)-binding domain and a C-terminal dimerization domain.


Pssm-ID: 467616 [Multi-domain]  Cd Length: 157  Bit Score: 45.61  E-value: 4.40e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275  34 IKVIINGAAKeIGRAAVVAVTKARGMELAGAVDNH--FVGEDIGLLCDmEEPLEIPVVSDLTMVLgsisQGKEVGVVIDF 111
Cdd:cd24146   1 IRVVVWGLGA-MGRGIARYLLEKPGLEIVGAVDRDpaKVGKDLGELGG-GAPLGVKVTDDLDAVL----AATKPDVVVHA 74

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15242275 112 T--DPSTVYENVKQATAFGmKSVV-------YVPRIKPETVSALSALC-------------DKATMGCLV 159
Cdd:cd24146  75 TtsFLADVAPQIERLLEAG-LNVIttceelfYPWARDPELAEELDALAkengvtvlgtgpgDVATAAIVV 143
 
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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