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PDBsum entry 1dxf

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protein ligands metals Protein-protein interface(s) links
Class ii aldolase PDB id
1dxf
Jmol
Contents
Protein chains
253 a.a. *
Ligands
PYR ×2
Metals
_MG ×2
Waters ×244
* Residue conservation analysis
PDB id:
1dxf
Name: Class ii aldolase
Title: 2-dehydro-3-deoxy-galactarate aldolase from escherichia coli in complex with pyruvate
Structure: 2-dehydro-3-deoxy-galactarate aldolase. Chain: a, b. Ec: 4.1.2.20
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: Hexamer (from PDB file)
Resolution:
2.6Å     R-factor:   0.173     R-free:   0.233
Authors: T.Izard,N.C.Blackwell
Key ref:
T.Izard and N.C.Blackwell (2000). Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism. EMBO J, 19, 3849-3856. PubMed id: 10921867 DOI: 10.1093/emboj/19.15.3849
Date:
05-Jan-00     Release date:   25-Aug-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P23522  (GARL_ECOLI) -  5-keto-4-deoxy-D-glucarate aldolase
Seq:
Struc:
256 a.a.
253 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.1.2.20  - 2-dehydro-3-deoxyglucarate aldolase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 2-dehydro-3-deoxy-D-glucarate = pyruvate + tartronate semialdehyde
2-dehydro-3-deoxy-D-glucarate
=
pyruvate
Bound ligand (Het Group name = PYR)
corresponds exactly
+ tartronate semialdehyde
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     glucarate catabolic process   3 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1093/emboj/19.15.3849 EMBO J 19:3849-3856 (2000)
PubMed id: 10921867  
 
 
Crystal structures of the metal-dependent 2-dehydro-3-deoxy-galactarate aldolase suggest a novel reaction mechanism.
T.Izard, N.C.Blackwell.
 
  ABSTRACT  
 
Carbon-carbon bond formation is an essential reaction in organic chemistry and the use of aldolase enzymes for the stereochemical control of such reactions is an attractive alternative to conventional chemical methods. Here we describe the crystal structures of a novel class II enzyme, 2-dehydro-3-deoxy-galactarate (DDG) aldolase from Escherichia coli, in the presence and absence of substrate. The crystal structure was determined by locating only four Se sites to obtain phases for 506 protein residues. The protomer displays a modified (alpha/beta)(8) barrel fold, in which the eighth alpha-helix points away from the beta-barrel instead of packing against it. Analysis of the DDG aldolase crystal structures suggests a novel aldolase mechanism in which a phosphate anion accepts the proton from the methyl group of pyruvate.
 
  Selected figure(s)  
 
Figure 3.
Figure 3 (A) Space filling representation of the hexameric DDG aldolase looking down the non-crystallographic dyad. Each of the six subunits is colored differently. (B) Cartoon drawing of DDG aldolase oligomer shown in the same orientation as in (A) illustrating the active site pocket location between two 3-fold-related protomers. For clarity, only four of the six protomers within the hexamer are shown. The two phosphates located in the active site pocket and the catalytic magnesium are shown in space filling representation. The active site pocket is mainly lined by residues belonging to one protomer. The 3-fold-related subunit makes contacts with the 'second' phosphate.
Figure 4.
Figure 4 Stereo views of ligands binding to DDG aldolase. The bonds of the ligands are shown in pink while the bonds of the enzyme are shown in white. For clarity, water molecules (drawn as red spheres) are not labeled. The magnesium site is shown and possible ligands coordinating the Mg^2+ are indicated. (A)–(D) are in the same orientation. (A) Residues in contact with the two phosphate anions bound to the active site pocket as seen in the substrate-free DDG aldolase structure. Final [A]-weighted F[o] – F[c] omit electron density map for ligands bound to the enzyme. The contour level of the electron density map is 3 and the resolution is 1.8 Å. Four solvent molecules and the catalytic magnesium interact with the 'first' phosphate and five water molecules are hydrogen bonded to the 'second' phosphate. Ser124' and Val125' belong to a 3-fold-related protomer. (B) Residues in contact with pyruvate. Final [A]-weighted F[o] – F[c] omit electron density map for pyruvate bound to the enzyme. The contour level of the electron density map is 3 and the resolution is 2.6 Å. The ligand's carbonyl and carboxyl reside 2.5 and 2.4 Å, respectively, away from the magnesium. All contacts are made by one subunit within the hexamer. (C) Superposition of the substrate-free structure (white) onto the aldolase–pyruvate complexed structure (gray) to illustrate the possible role of the 'second' phosphate in the reaction mechanism (gray dotted line). The anion's oxygen is 3.4 Å away from the methyl carbon atom. The current distance of 3.9 Å between Arg75 and the 'second' phosphate is easily decreased to hydrogen bonding distance by a slight side chain movement without steric hindrance and/or by moving the 'second' phosphate deeper into the active site. (D) Modeling of the condensed substrate, DDG, into the active site based upon the aldolase–pyruvate structure. The carboxylate at C6 of DDG fills the cavity occupied by the 'second' phosphate. A possible role during catalysis for the solvent molecule bridging the ligand's O4 and His50 is indicated (gray dotted line).
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 3849-3856) copyright 2000.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21083941 P.Sharma, B.Kumar, Y.Gupta, N.Singhal, V.M.Katoch, K.Venkatesan, and D.Bisht (2010).
Proteomic analysis of streptomycin resistant and sensitive clinical isolates of Mycobacterium tuberculosis.
  Proteome Sci, 8, 59.  
18754693 J.F.Rakus, A.A.Fedorov, E.V.Fedorov, M.E.Glasner, B.K.Hubbard, J.D.Delli, P.C.Babbitt, S.C.Almo, and J.A.Gerlt (2008).
Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase.
  Biochemistry, 47, 9944-9954.
PDB codes: 2i5q 3box 3cxo
18505728 S.Watanabe, M.Saimura, and K.Makino (2008).
Eukaryotic and bacterial gene clusters related to an alternative pathway of nonphosphorylated L-rhamnose metabolism.
  J Biol Chem, 283, 20372-20382.  
19039353 W.L.Kelly (2008).
Intramolecular cyclizations of polyketide biosynthesis: mining for a "Diels-Alderase"?
  Org Biomol Chem, 6, 4483-4493.  
17457413 J.M.Serafimov, H.C.Lehmann, H.Oikawa, and D.Hilvert (2007).
Active site mutagenesis of the putative Diels-Alderase macrophomate synthase.
  Chem Commun (Camb), (), 1701-1703.  
17559390 S.V.Smirnov, N.N.Samsonova, A.E.Novikova, N.G.Matrosov, N.Y.Rushkevich, T.Kodera, J.Ogawa, H.Yamanaka, and S.Shimizu (2007).
A novel strategy for enzymatic synthesis of 4-hydroxyisoleucine: identification of an enzyme possessing HMKP (4-hydroxy-3-methyl-2-keto-pentanoate) aldolase activity.
  FEMS Microbiol Lett, 273, 70-77.  
16950779 S.Watanabe, N.Shimada, K.Tajima, T.Kodaki, and K.Makino (2006).
Identification and characterization of L-arabonate dehydratase, L-2-keto-3-deoxyarabonate dehydratase, and L-arabinolactonase involved in an alternative pathway of L-arabinose metabolism. Novel evolutionary insight into sugar metabolism.
  J Biol Chem, 281, 33521-33536.  
  17142914 X.Li, H.Huang, X.Song, Y.Wang, H.Xu, M.Teng, and W.Gong (2006).
Purification, crystallization and preliminary crystallographic studies on 2-dehydro-3-deoxygalactarate aldolase from Leptospira interrogans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1269-1270.  
  16511168 D.Rea, V.Fülöp, T.D.Bugg, and D.I.Roper (2005).
Expression, purification and preliminary crystallographic analysis of 2,4-dihydroxy-hepta-2-ene-1,7-dioate aldolase (HpcH) from Escherichia coli C.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 821-824.  
15612933 T.Franza, B.Mahé, and D.Expert (2005).
Erwinia chrysanthemi requires a second iron transport route dependent of the siderophore achromobactin for extracellular growth and plant infection.
  Mol Microbiol, 55, 261-275.  
15381846 S.Namboori, N.Mhatre, S.Sujatha, N.Srinivasan, and S.B.Pandit (2004).
Enhanced functional and structural domain assignments using remote similarity detection procedures for proteins encoded in the genome of Mycobacterium tuberculosis H37Rv.
  J Biosci, 29, 245-259.  
14699122 T.Izard, and J.Sygusch (2004).
Induced fit movements and metal cofactor selectivity of class II aldolases: structure of Thermus aquaticus fructose-1,6-bisphosphate aldolase.
  J Biol Chem, 279, 11825-11833.
PDB codes: 1rv8 1rvg
15213379 T.Ose, K.Watanabe, M.Yao, M.Honma, H.Oikawa, and I.Tanaka (2004).
Structure of macrophomate synthase.
  Acta Crystallogr D Biol Crystallogr, 60, 1187-1197.  
12764229 B.A.Manjasetty, J.Powlowski, and A.Vrielink (2003).
Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate.
  Proc Natl Acad Sci U S A, 100, 6992-6997.
PDB code: 1nvm
12842039 B.N.Chaudhuri, M.R.Sawaya, C.Y.Kim, G.S.Waldo, M.S.Park, T.C.Terwilliger, and T.O.Yeates (2003).
The crystal structure of the first enzyme in the pantothenate biosynthetic pathway, ketopantoate hydroxymethyltransferase, from M tuberculosis.
  Structure, 11, 753-764.
PDB code: 1oy0
12837791 F.Schmitzberger, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily.
  J Bacteriol, 185, 4163-4171.  
12906829 F.von Delft, T.Inoue, S.A.Saldanha, H.H.Ottenhof, F.Schmitzberger, L.M.Birch, V.Dhanaraj, M.Witty, A.G.Smith, T.L.Blundell, and C.Abell (2003).
Structure of E. coli ketopantoate hydroxymethyl transferase complexed with ketopantoate and Mg2+, solved by locating 160 selenomethionine sites.
  Structure, 11, 985-996.
PDB code: 1m3u
12634789 T.Ose, K.Watanabe, T.Mie, M.Honma, H.Watanabe, M.Yao, H.Oikawa, and I.Tanaka (2003).
Insight into a natural Diels-Alder reaction from the structure of macrophomate synthase.
  Nature, 422, 185-189.
PDB code: 1izc
12454498 A.Wright, A.Blewett, V.Fulop, R.Cooper, S.Burrows, C.Jones, and D.Roper (2002).
Expression, purification, crystallization and preliminary characterization of an HHED aldolase homologue from Escherichia coli K12.
  Acta Crystallogr D Biol Crystallogr, 58, 2191-2193.  
12324329 M.J.Hernáez, B.Floriano, J.J.Ríos, and E.Santero (2002).
Identification of a hydratase and a class II aldolase involved in biodegradation of the organic solvent tetralin.
  Appl Environ Microbiol, 68, 4841-4846.  
11976494 M.Kroemer, and G.E.Schulz (2002).
The structure of L-rhamnulose-1-phosphate aldolase (class II) solved by low-resolution SIR phasing and 20-fold NCS averaging.
  Acta Crystallogr D Biol Crystallogr, 58, 824-832.
PDB code: 1gt7
11134944 L.Pedersen, G.R.Andersen, C.R.Knudsen, T.G.Kinzy, and J.Nyborg (2001).
Crystallization of the yeast elongation factor complex eEF1A-eEF1B alpha.
  Acta Crystallogr D Biol Crystallogr, 57, 159-161.  
11173490 V.Sauvé, and J.Sygusch (2001).
Crystallization and preliminary X-ray analysis of native and selenomethionine fructose-1,6-bisphosphate aldolase from Thermus aquaticus.
  Acta Crystallogr D Biol Crystallogr, 57, 310-313.  
11849940 W.D.Fessner, and V.Helaine (2001).
Biocatalytic synthesis of hydroxylated natural products using aldolases and related enzymes.
  Curr Opin Biotechnol, 12, 574-586.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.