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Overview for MACiE Entry M0059

Version history

General Information

EC Number: 4.2.3.4 (A member of the Lyases, Carbon-oxygen lyases, Acting on phosphates)

Enzyme Name: 3-dehydroquinate synthase

Biological Species: Emericella nidulans (Fungus)

Catalytic Chain UniprotKB Accession Codes:

  • P07547 - Shikimate dehydrogenase

Representative PDB Code: 1dqs - CRYSTAL STRUCTURE OF DEHYDROQUINATE SYNTHASE (DHQS)COMPLEXED WITH CARBAPHOSPHONATE, NAD+ AND ZN2+ (Resolution = 1.80 Å).

Catalytic CATH Codes:

"Other" CATH Codes:

Display structure information

Overall Reaction:

Image of 7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate (DAHP)

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Image of 3-dehydroquinate

Image of phosphate

7-phospho-2-dehydro-3-deoxy-D-arabino-heptonate (DAHP)
C04691
CHEBI:58394
3-dehydroquinate
C00944
CHEBI:32364
phosphate
C00009
CHEBI:18367

Overall Comment: In KEGG the substrate is linear.


View similar reactions


Stepwise Description of the Reaction

Step 1His275 (activated by water) deprotonates a water molecule, which in turn deprotonates the alcohol of the sugar substrate at the C5 position. This forms a ketone group, and causes elimination of a hydride ion, which adds to NAD+.
Step 2The phosphate deprotonates the C4 position, causing self elimination.
Step 3NADH eliminates a hydride ion, which adds to the C5 position of the sugar ring, causing the ketone to be reduced and deprotonates water, which deprotonates the His275.
Step 4Glu260 deprotonates water, which deprotonates the C2 alcohol of the sugar, cleaving the ring.
Step 5The newly formed oxyanion initiates double bond rearrangement, and causes an intramolecular nucleophilic attack on the keto-group formed previously, reforming the ring structure.

View similar reactions (composite manual annotation)


Catalytic Residues Involved

Type Number Chain Location of Function
Lys 152 A Side Chain
Lys 250 A Side Chain
Glu 260 A Side Chain
Arg 264 A Side Chain
Asn 268 A Side Chain
His 275 A Side Chain

Organic Cofactors for M0059

Type Identity Chain
NAD NAD 400 A Overview

Metal Cofactors for M0059

Type Het group Number Chain
zinc ZN 402 A Overview

References

  1. E. P. Carpenter et al. (1998), Nature, 394, 299-302. Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis.
    Medline: 9685163

Homologue information for M0059 (1dqs)

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
M0312 glycerol dehydrogenase
1.1.1.6
1kq3 1.20.1090.10
3.40.50.1970
0.09490.1222Compare

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

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3-dehydroquinate synthase activity (molecular function)
cytoplasm (cellular component)
aromatic amino acid family biosynthetic process (biological process)
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