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PDBsum entry 1qq5

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1qq5
Jmol
Contents
Protein chains
245 a.a. *
Ligands
FMT ×2
Waters ×571
* Residue conservation analysis
PDB id:
1qq5
Name: Hydrolase
Title: Structure of l-2-haloacid dehalogenase from xanthobacter autotrophicus
Structure: Protein (l-2-haloacid dehalogenase). Chain: a, b. Other_details: substrate analogue formate present in both active sites
Source: Xanthobacter autotrophicus. Organism_taxid: 280. Strain: gj10
Biol. unit: Dimer (from PQS)
Resolution:
1.52Å     R-factor:   0.204     R-free:   0.232
Authors: I.S.Ridder,H.J.Rozeboom,K.H.Kalk,B.W.Dijkstra
Key ref:
I.S.Ridder et al. (1999). Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase. J Biol Chem, 274, 30672-30678. PubMed id: 10521454 DOI: 10.1074/jbc.274.43.30672
Date:
10-Jun-99     Release date:   25-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q60099  (HAD_XANAU) -  (S)-2-haloacid dehalogenase
Seq:
Struc:
253 a.a.
245 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.8.1.2  - (S)-2-haloacid dehalogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
2-Haloacid Dehalogenase (configuration-inverting)
      Reaction: (S)-2-haloacid + H2O = (R)-2-hydroxyacid + halide
(S)-2-haloacid
Bound ligand (Het Group name = FMT)
matches with 50.00% similarity
+ H(2)O
= (R)-2-hydroxyacid
+ halide
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     hydrolase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.274.43.30672 J Biol Chem 274:30672-30678 (1999)
PubMed id: 10521454  
 
 
Crystal structures of intermediates in the dehalogenation of haloalkanoates by L-2-haloacid dehalogenase.
I.S.Ridder, H.J.Rozeboom, K.H.Kalk, B.W.Dijkstra.
 
  ABSTRACT  
 
The L-2-haloacid dehalogenase from the 1,2-dichloroethane-degrading bacterium Xanthobacter autotrophicus GJ10 catalyzes the hydrolytic dehalogenation of small L-2-haloalkanoates to their corresponding D-2-hydroxyalkanoates, with inversion of the configuration at the C(2) atom. The structure of the apoenzyme at pH 8 was refined at 1.5-A resolution. By lowering the pH, the catalytic activity of the enzyme was considerably reduced, allowing the crystal structure determination of the complexes with L-2-monochloropropionate and monochloroacetate at 1.7 and 2.1 A resolution, respectively. Both complexes showed unambiguous electron density extending from the nucleophile Asp(8) to the C(2) atom of the dechlorinated substrates corresponding to a covalent enzyme-ester reaction intermediate. The halide ion that is cleaved off is found in line with the Asp(8) Odelta1-C(2) bond in a halide-stabilizing cradle made up of Arg(39), Asn(115), and Phe(175). In both complexes, the Asp(8) Odelta2 carbonyl oxygen atom interacts with Thr(12), Ser(171), and Asn(173), which possibly constitute the oxyanion hole in the hydrolysis of the ester bond. The carboxyl moiety of the substrate is held in position by interactions with Ser(114), Lys(147), and main chain NH groups. The L-2-monochloropropionate CH(3) group is located in a small pocket formed by side chain atoms of Lys(147), Asn(173), Phe(175), and Asp(176). The size and position of the pocket explain the stereospecificity and the limited substrate specificity of the enzyme. These crystallographic results demonstrate that the reaction of the enzyme proceeds via the formation of a covalent enzyme-ester intermediate at the nucleophile Asp(8).
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Two conformations of residues 208-213 of molecules A and B at the dimerization interface.
Figure 3.
Fig. 3. Schematic representation of the interactions in the covalent complexes of DhlB with L-2-monochloropropionate (A) and monochloroacetate (B). Hydrogen bonding interactions with the covalent intermediate and the chloride ion are represented by dashed lines, and other interactions are represented by dotted lines with interatomic distances in Å.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 30672-30678) copyright 1999.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20372740 D.O'Hagan, and J.W.Schmidberger (2010).
Enzymes that catalyse SN2 reaction mechanisms.
  Nat Prod Rep, 27, 900-918.  
19039518 C.A.Rye, M.N.Isupov, A.A.Lebedev, and J.A.Littlechild (2009).
Biochemical and structural studies of a L: -haloacid dehalogenase from the thermophilic archaeon Sulfolobus tokodaii.
  Extremophiles, 13, 179-190.
PDB codes: 2w11 2w43
19154134 J.Dai, L.Finci, C.Zhang, S.Lahiri, G.Zhang, E.Peisach, K.N.Allen, and D.Dunaway-Mariano (2009).
Analysis of the structural determinants underlying discrimination between substrate and solvent in beta-phosphoglucomutase catalysis.
  Biochemistry, 48, 1984-1995.
PDB code: 3fm9
19879837 Y.Shi (2009).
Serine/threonine phosphatases: mechanism through structure.
  Cell, 139, 468-484.  
  18084090 B.V.Le, H.S.Lee, Y.Cho, S.G.Kang, D.Y.Kim, Y.G.Kim, and K.K.Kim (2007).
Crystallization and preliminary X-ray studies of TON_1713 from Thermococcus onnurineus NA1, a putative member of the haloacid dehalogenase superfamily.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 1048-1050.  
16815921 K.N.Rao, D.Kumaran, J.Seetharaman, J.B.Bonanno, S.K.Burley, and S.Swaminathan (2006).
Crystal structure of trehalose-6-phosphate phosphatase-related protein: biochemical and biological implications.
  Protein Sci, 15, 1735-1744.
PDB code: 1u02
16385007 R.Arai, M.Kukimoto-Niino, C.Kuroishi, Y.Bessho, M.Shirouzu, and S.Yokoyama (2006).
Crystal structure of the probable haloacid dehalogenase PH0459 from Pyrococcus horikoshii OT3.
  Protein Sci, 15, 373-377.
PDB code: 1x42
16309386 D.B.Janssen, I.J.Dinkla, G.J.Poelarends, and P.Terpstra (2005).
Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities.
  Environ Microbiol, 7, 1868-1882.  
  16511085 H.Wang, H.Pang, Y.Ding, Y.Li, X.Wu, and Z.Rao (2005).
Purification, crystallization and preliminary X-ray diffraction analysis of human enolase-phosphatase E1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 521-523.  
  16511015 J.W.Schmidberger, A.J.Oakley, J.S.Tsang, and M.C.Wilce (2005).
Purification, crystallization and preliminary crystallographic analysis of DehIVa, a dehalogenase from Burkholderia cepacia MBA4.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 271-273.  
15146493 E.C.Meng, B.J.Polacco, and P.C.Babbitt (2004).
Superfamily active site templates.
  Proteins, 55, 962-976.  
12824492 D.H.Shin, A.Roberts, J.Jancarik, H.Yokota, R.Kim, D.E.Wemmer, and S.H.Kim (2003).
Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima.
  Protein Sci, 12, 1464-1472.
PDB code: 1nf2
14675551 R.M.de Jong, and B.W.Dijkstra (2003).
Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon-halogen bond.
  Curr Opin Struct Biol, 13, 722-730.  
12220496 E.A.Galburt, J.Pelletier, G.Wilson, and B.L.Stoddard (2002).
Structure of a tRNA repair enzyme and molecular biology workhorse: T4 polynucleotide kinase.
  Structure, 10, 1249-1260.
PDB code: 1ltq
11807265 S.D.Lahiri, G.Zhang, P.Radstrom, D.Dunaway-Mariano, and K.N.Allen (2002).
Crystallization and preliminary X-ray diffraction studies of beta-phosphoglucomutase from Lactococcus lactus.
  Acta Crystallogr D Biol Crystallogr, 58, 324-326.  
11404103 D.B.Janssen, J.E.Oppentocht, and G.J.Poelarends (2001).
Microbial dehalogenation.
  Curr Opin Biotechnol, 12, 254-258.  
11418568 G.J.Poelarends, R.Saunier, and D.B.Janssen (2001).
trans-3-Chloroacrylic acid dehalogenase from Pseudomonas pavonaceae 170 shares structural and mechanistic similarities with 4-oxalocrotonate tautomerase.
  J Bacteriol, 183, 4269-4277.  
11337417 M.G.Palmgren (2001).
PLANT PLASMA MEMBRANE H+-ATPases: Powerhouses for Nutrient Uptake.
  Annu Rev Plant Physiol Plant Mol Biol, 52, 817-845.  
10975456 A.W.Munro, P.Taylor, and M.D.Walkinshaw (2000).
Structures of redox enzymes.
  Curr Opin Biotechnol, 11, 369-376.  
10679381 G.A.Petsko, and D.Ringe (2000).
Observation of unstable species in enzyme-catalyzed transformations using protein crystallography.
  Curr Opin Chem Biol, 4, 89-94.  
11114513 I.Schlichting, and K.Chu (2000).
Trapping intermediates in the crystal: ligand binding to myoglobin.
  Curr Opin Struct Biol, 10, 744-752.  
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.