PDBsum entry 2ze3

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Isomerase PDB id
Protein chain
275 a.a. *
Waters ×253
* Residue conservation analysis
PDB id:
Name: Isomerase
Title: Crystal structure of dfa0005 complexed with alpha-ketoglutar novel member of the icl/pepm superfamily from alkali-tolera deinococcus ficus
Structure: Dfa0005. Chain: a. Engineered: yes
Source: Deinococcus ficus. Organism_taxid: 317577. Expressed in: escherichia coli. Expression_system_taxid: 562
1.65Å     R-factor:   0.223     R-free:   0.234
Authors: C.J.Liao,K.H.Chin,S.H.Chou
Key ref:
C.J.Liao et al. (2008). Crystal structure of DFA0005 complexed with alpha-ketoglutarate: A novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus. Proteins, 73, 362-371. PubMed id: 18433062 DOI: 10.1002/prot.22071
05-Dec-07     Release date:   12-Aug-08    
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Protein chain
No UniProt id for this chain
Struc: 275 a.a.
Key:    Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     catalytic activity     1 term  


DOI no: 10.1002/prot.22071 Proteins 73:362-371 (2008)
PubMed id: 18433062  
Crystal structure of DFA0005 complexed with alpha-ketoglutarate: A novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus.
C.J.Liao, K.H.Chin, C.H.Lin, P.S.Tsai, P.C.Lyu, C.C.Young, A.H.Wang, S.H.Chou.
The crystal structure of the DFA0005 protein complexed with alpha-ketoglutarate (AKG) from an alkali-tolerant bacterium Deinococcus ficus has been determined to a resolution of 1.62 A. The monomer forms an incomplete alpha7/beta8 barrel with a protruding alpha8 helix that interacts extensively with another subunit to form a stable dimer of two complete alpha8/beta8 barrels. The dimer is further stabilized by four glycerol molecules situated at the interface. One unique AKG ligand binding pocket per subunit is detected. Fold match using the DALI and SSE servers identifies DFA0005 as belonging to the isocitrate lyase/phosphoenolpyruvate mutase (ICL/PEPM) superfamily. However, further detailed structural and sequence comparison with other members in this superfamily and with other families containing AKG ligand indicate that DFA0005 protein exhibits considerable distinguishing features of its own and can be considered a novel member in this ICL/PEPM superfamily. Proteins 2008. (c) 2008 Wiley-Liss, Inc.
  Selected figure(s)  
Figure 2.
Figure 2. Multiple structure and sequence alignments of DFA0005 with other typical proteins in the ICL/PEPM superfamily generated by the MUSTANG[31] and formatted by the Alscript.[36] MICL, ICL, PEPH, PEPM stand for 2 -methylisocitrate lyase, isocitrate lyase, phosphoenolpyruvate hydrolase, and phosphoenolpyruvate mutase, respectively. Identical residues are shown in red letters and highly conserved residues in blue letters. The secondary structure elements for -helices (horizontal blue cylinders) and -strands (horizontal red arrows) are also shown on the top along with their annotations. Conserved amino acid residues for binding with the similar head moiety are marked by solid red circles, while those for binding with the tail moiety of AKG in DFA0005 are marked by solid blue circles. The critical residues partially determining the binding orientation of ligands in the ICL/PEPM superfamily are shown in white letters with a red background. The two signature amino acid patches conserved for the typical ICL/MICL or PEPM/PEPH families in the 2- 2 and L4 regions are boxed. The 2 - 2 (L2), 4- 4 (L4), and 5- 5 (L5) loops are also annotated and connected by green lines.
Figure 4.
Figure 4. (a) The stereo picture of the unique AKG binding pocket and water channel of DFA0005. The entry of the channel on top of the -barrel is indicated by a blue arrow, with the fourteen well visible water molecules and AKG ligand circled in blue. The water oxygen atoms are drawn in solid blue circles and the AKG ligand in ball-and-stick. (b) The close-up of the circled region in Figure 4(a). The H-bonds between the water molecules and the surrounding amino acid residues are connected by gray dotted arrows. The side chain oxygen atoms of Glu87 are located in the entry of water channel and participate extensively in the H-bonding network. The two deeply buried water molecules are indicated by blue arrows. The surrounding -strands are also annotated. (c) The scheme of the AKG binding pocket drawn by Ligplot.[37] The AKG is traced in a curved green line. The oxygen atoms are colored in red, while those of the seven water oxygen atoms in light blue. H-bonds are connected in green dotted lines. Conserved amino acids contacting the head -ketocarboxylate moiety among the ICL/PEPM superfamily are circled in red, while those amino acids located in the 3, 4, 7, and 8 strands and contact the tail carboxylate of AKG in DFA0005 are indicated by arrows. The critical residue in position 41 is labeled in blue letters.
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 73, 362-371) copyright 2008.  
  Figures were selected by an automated process.