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330  structures 4601  species 1  interaction 10473  sequences 24  architectures

Family: DHDPS (PF00701)

Summary: Dihydrodipicolinate synthetase family

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This is the Wikipedia entry entitled "Dihydrodipicolinate synthase". More...

Dihydrodipicolinate synthase Edit Wikipedia article

dihydrodipicolinate synthase
Identifiers
EC number 4.3.3.7
CAS number 9055-59-8
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO
Dihydrodipicolinate synthetase family
PDB 1xky EBI.jpg
crystal structure of dihydrodipicolinate synthase dapa-2 (ba3935) from bacillus anthracis at 1.94a resolution.
Identifiers
Symbol DHDPS
Pfam PF00701
Pfam clan CL0036
InterPro IPR002220
PROSITE PDOC00569
SCOP 1dhp
SUPERFAMILY 1dhp

In enzymology, a dihydrodipicolinate synthase (EC 4.3.3.7) is an enzyme that catalyzes the chemical reaction

L-aspartate 4-semialdehyde + pyruvate \rightleftharpoons (S)-2,3-dihydropyridine-2,6-dicarboxylate + 2 H2O

Thus, the two substrates of this enzyme are L-aspartate 4-semialdehyde and pyruvate, whereas its two products are (S)-2,3-dihydropyridine-2,6-dicarboxylate and H2O.

This enzyme belongs to the family of lyases, specifically the hydro-lyases, which cleave carbon-oxygen bonds. The systematic name of this enzyme class is L-aspartate-4-semialdehyde hydro-lyase [adding pyruvate and cyclizing; (S)-2,3-dihydropyridine-2,6-dicarboxylate-forming]. Other names in common use include dihydropicolinate synthetase (DHDPS), dihydrodipicolinic acid synthase, L-aspartate-4-semialdehyde hydro-lyase (adding pyruvate and, and cyclizing). This enzyme participates in lysine biosynthesis.

Dihydropicolinate synthase is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes, and higher plants. The enzyme catalyses the condensation of L-aspartate-beta-semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff base with a lysine residue.[1] Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (EC 4.1.3.3) (protein NanA), which catalyses the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein MosA,[2] which is involved in the biosynthesis of the rhizopine 3-O-methyl-scyllo-inosamine; and E. coli hypothetical protein YjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry.[1] Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.

Structural studies

As of late 2007, 16 structures have been solved for this class of enzymes, with PDB accession codes 1DHP, 1O5K, 1S5T, 1S5V, 1S5W, 1XKY, 1XL9, 1XXX, 1YXC, 1YXD, 2A6L, 2A6N, 2ATS, 2D5K, 2EHH, and 2PCQ.

References

  1. ^ a b Mirwaldt C, Korndorfer I, Huber R (February 1995). "The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution". J. Mol. Biol. 246 (1): 227–39. doi:10.1006/jmbi.1994.0078. PMID 7853400. 
  2. ^ Murphy PJ, Trenz SP, Grzemski W, De Bruijn FJ, Schell J (August 1993). "The Rhizobium meliloti rhizopine mos locus is a mosaic structure facilitating its symbiotic regulation". J. Bacteriol. 175 (16): 5193–204. PMC 204987. PMID 8349559. 

Further reading

  • Shedlarski JG, Gilvarg C (1970). "The pyruvate-aspartic semialdehyde condensing enzyme of Escherichia coli". J. Biol. Chem. 245 (6): 1362–73. PMID 4910051. 
  • Yugari Y, Gilvarg C (1965). "The condensation step in diaminopimelate synthesis". J. Biol. Chem. 240 (12): 4710–6. PMID 5321309. 

This article incorporates text from the public domain Pfam and InterPro IPR002220

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Dihydrodipicolinate synthetase family Provide feedback

This family has a TIM barrel structure.

Literature references

  1. Izard T, Lawrence MC, Malby RL, Lilley GG, Colman PM; , Structure 1994;2:361-369.: The three-dimensional structure of N-acetylneuraminate lyase from Escherichia coli. PUBMED:8081752 EPMC:8081752


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002220

Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue [PUBMED:7853400]. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [PUBMED:8349559], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry [PUBMED:7853400]. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(13)
Full
(10473)
Representative proteomes NCBI
(7818)
Meta
(5086)
RP15
(799)
RP35
(1639)
RP55
(2295)
RP75
(2809)
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Format an alignment

  Seed
(13)
Full
(10473)
Representative proteomes NCBI
(7818)
Meta
(5086)
RP15
(799)
RP35
(1639)
RP55
(2295)
RP75
(2809)
Alignment:
Format:
Order:
Sequence:
Gaps:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(13)
Full
(10473)
Representative proteomes NCBI
(7818)
Meta
(5086)
RP15
(799)
RP35
(1639)
RP55
(2295)
RP75
(2809)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_557 (release 2.1)
Previous IDs: none
Type: Domain
Author: Bateman A, Griffiths-Jones SR
Number in seed: 13
Number in full: 10473
Average length of the domain: 284.20 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 95.11 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.1 22.1
Trusted cut-off 22.1 22.2
Noise cut-off 21.9 22.0
Model length: 289
Family (HMM) version: 17
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

DHDPS

Structures

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 DHDPS domain has been found. There are 330 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 seqence.

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