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89  structures 6901  species 0  interactions 8327  sequences 24  architectures

Family: DapB_C (PF05173)

Summary: Dihydrodipicolinate reductase, C-terminus

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Dihydrodipicolinate reductase, C-terminus Provide feedback

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.

Literature references

  1. Reddy SG, Scapin G, Blanchard JS; , Biochemistry 1996;35:13294-13302.: Interaction of pyridine nucleotide substrates with Escherichia coli dihydrodipicolinate reductase: thermodynamic and structural analysis of binary complexes. PUBMED:8873595 EPMC:8873595

  2. Scapin G, Reddy SG, Zheng R, Blanchard JS; , Biochemistry 1997;36:15081-15088.: Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate. PUBMED:9398235 EPMC:9398235

  3. Scapin G, Blanchard JS, Sacchettini JC; , Biochemistry 1995;34:3502-3512.: Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase. PUBMED:7893645 EPMC:7893645

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR022663

Dihydrodipicolinate reductase catalyzes the second step in the biosynthesis of diaminopimelic acid and lysine, the NAD or NADP-dependent reduction of 2,3-dihydrodipicolinate into 2,3,4,5-tetrahydrodipicolinate [ PUBMED:8873595 , PUBMED:9398235 , PUBMED:7893645 ].

In Escherichia coli and Mycobacterium tuberculosis, dihydrodipicolinate reductase has equal specificity for NADH and NADPH, however in Thermotoga maritima there it has a greater affinity for NADPH [ PUBMED:18250105 ]. In addition, the enzyme is inhibited by high concentrations of its substrate, which consequently acts as a feedback control on the lysine biosynthesis pathway. In T. maritima, the enzyme also lacks N-terminal and C-terminal loops which are present in enzyme of the former two organisms.

This entry represents the C-terminal region of Dihydrodipicolinate reductase.

Gene Ontology

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Domain organisation

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Pfam Clan

This family is a member of clan GADPH_aa-bio_dh (CL0139), which has the following description:

This clan contains the C terminal domains of dehydrogenase enzymes involved in the biosynthesis of arginine, aspartate and aspartate derived amino acids. It also contains the C terminal domain of GAPDH, a dehydrogenase involved in glycolysis and gluconeogenesis.

The clan contains the following 17 members:

AcetDehyd-dimer Biliv-reduc_cat DapB_C DAPDH_C DUF108 DXP_redisom_C G6PD_C GFO_IDH_MocA_C GFO_IDH_MocA_C2 Gp_dh_C Homoserine_dh Inos-1-P_synth ox_reductase_C Oxidoreduct_C OxRdtase_C Sacchrp_dh_C Semialdhyde_dhC


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Curation and family details

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Seed source: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Studholme DJ
Number in seed: 557
Number in full: 8327
Average length of the domain: 134.20 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 51.26 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.8 20.9
Noise cut-off 20.5 20.3
Model length: 121
Family (HMM) version: 16
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Species distribution

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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the DapB_C domain has been found. There are 89 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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