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Overview for MACiE Entry M0267

Version history

General Information

EC Number: 4.2.1.52 (A member of the Lyases, Carbon-oxygen lyases, Hydro-lyases)

Enzyme Name: dihydrodipicolinate synthase

Biological Species: Escherichia coli (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

  • P0A6L2 - Dihydrodipicolinate synthase

Representative PDB Code: 1dhp - DIHYDRODIPICOLINATE SYNTHASE (Resolution = 2.30 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of L-aspartate beta semi aldehyde (hydrate)

Image of Pyruvate

right arrow

Image of (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid

Image of water

L-aspartate beta semi aldehyde (hydrate)
X00125
Pyruvate
C00022
CHEBI:15361
(4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinic acid
X00126
2 water
C00001
CHEBI:15377

View similar reactions


Stepwise Description of the Reaction

Step 1Lys161 acts as a nucleophile towards the keto group of the pyruvate substrate, forming a covalently bound enzyme-substrate intermediate. The pyruvate is polarised by the presence of the main chain carbonyl of Ile203, increasing its electrophilicity.
Step 2Proton transfer activates Schiff base formation in the next reaction step.
Step 3Elimination of water results in Schiff base formation.
Step 4The covalently bound lysine abstracts a proton from the terminal carbon to form the ene tautomer.
Step 5L-aspartate semi aldehyde is thought to enter the active site in the hydrate form. It then undergoes reversible dehydration to form the protonated aldehyde form.
Step 6The enamine tautomer of the Schiff base adds to the dehydrated L-aspartate semi aldehyde in a conjugate nucleophilic attack.
Step 7A 6-exo-tet cyclisation (Baldwin's classification) occurs in the enzyme-substrate intermediate.
Step 8Proton transfer is mediated through Tyr133.
Step 9The product is formed and the active site is regenerated for further catalysis.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Lys 161 A Side Chain
Tyr 133 A Side Chain
Ile 203 A Main Chain Carbonyl

References

  1. S. Blickling et al. (1996), Biochemistry, 36, 24-33. Reaction Mechanism of Escherichia coli Dihydrodipicolinate Synthase Investigated by X-ray Crystallography and NMR Spectroscopy.
    Medline: 8993314
  2. R. Dobson et al. (2008), Protein Sci., 17, 2080-2090. Conserved main-chain peptide distortions: A proposed role for Ile203 in catalysis by dihydrodipicolinate synthase.
    Medline: 18787203

Homologue information for M0267 (1dhp)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)



Entries with at least one Catalytic CATH code in common (different mechanisms):

MACiE Entry Enzyme Name
EC Number
PDB code CATH code Composite
Reaction Similarity
Catalytic Machinery
Similarity
M0102 L-lactate dehydrogenase (cytochrome)
1.1.2.3
1fcb 3.20.20.70
0.49230.1967Compare
M0108 2,4-dienoyl-CoA reductase (NADPH)
1.3.1.34
1ps9 3.20.20.70
0.44260.1516Compare
M0109 dihydroorotate oxidase
1.3.3.1
1d3g 3.20.20.70
0.44440.1499Compare
M0111 glutamate synthase (ferredoxin)
1.4.7.1
1ofd 3.20.20.70
0.58210.0785Compare
M0114 trimethylamine dehydrogenase
1.5.8.2
2tmd 3.20.20.70
0.36360.1967Compare
M0319 NADPH dehydrogenase
1.6.99.1
1oya 3.20.20.70
0.30660.0999Compare
M0148 transaldolase
2.2.1.2
1onr 3.20.20.70
0.29070.1499Compare
M0008 nicotinate-nucleotide diphosphorylase (carboxylating)
2.4.2.19
1qpr 3.20.20.70
0.22850.1499Compare
M0243 pyridoxine 5'-phosphate synthase
2.6.99.2
1ho1 3.20.20.70
0.50760Compare
M0050 orotidine-5'-phosphate decarboxylase
4.1.1.23
1dbt 3.20.20.70
0.06060.1563Compare
M0252 indole-3-glycerol-phosphate synthase
4.1.1.48
1igs 3.20.20.70
0.440.1636Compare
M0236 3-dehydro-L-gulonate-6-phosphate decarboxylase
4.1.1.85
1q6l 3.20.20.70
0.2380.1702Compare
M0052 fructose-bisphosphate aldolase (Class II)
4.1.2.13
1b57 3.20.20.70
0.30760Compare
M0222 fructose-bisphosphate aldolase (Class I)
4.1.2.13
2qut 3.20.20.70
0.28690.2669Compare
M0054 3-dehydroquinate dehydratase (type I)
4.2.1.10
1qfe 3.20.20.70
0.50660.18Compare
M0230 porphobilinogen synthase
4.2.1.24
1gzg 3.20.20.70
0.58190.3808Compare
M0270 ribulose-phosphate 3-epimerase
5.1.3.1
1h1z 3.20.20.70
0.21870.0148Compare
M0324 triosephosphate isomerase
5.3.1.1
1tph 3.20.20.70
0.12820.1499Compare
M0223 pyruvate carboxylase
6.4.1.1
2qf7 3.20.20.70
0.62350.1426Compare

View a comparison of the other reactions in MACiE with the CATH domain 3.20.20.70


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ
Link to EzCatDB

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catalytic activity (molecular function)
metabolic process (biological process)
4-hydroxy-tetrahydrodipicolinate synthase (molecular function)
lyase activity (molecular function)
diaminopimelate biosynthetic process (biological process)
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