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PDBsum entry 2oww

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Transferase PDB id
2oww
Jmol
Contents
Protein chain
499 a.a. *
Ligands
ACR
G4D
MLI
GOL ×2
Waters ×321
* Residue conservation analysis
PDB id:
2oww
Name: Transferase
Title: Covalent intermediate in amylomaltase in complex with the ac analog 4-deoxyglucose
Structure: 4-alpha-glucanotransferase. Chain: a. Fragment: amylomaltase. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 274. Gene: malq. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.20Å     R-factor:   0.200     R-free:   0.240
Authors: T.R.M.Barends,J.B.Bultema,T.Kaper,M.J.E.C.Van Der Maarel, L.Dijkhuizen,B.W.Dijkstra
Key ref:
T.R.Barends et al. (2007). Three-way stabilization of the covalent intermediate in amylomaltase, an alpha-amylase-like transglycosylase. J Biol Chem, 282, 17242-17249. PubMed id: 17420245 DOI: 10.1074/jbc.M701444200
Date:
17-Feb-07     Release date:   03-Apr-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O87172  (MALQ_THETH) -  4-alpha-glucanotransferase
Seq:
Struc:
500 a.a.
499 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.25  - 4-alpha-glucanotransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Transfers a segment of a (1,4)-alpha-D-glucan to a new 4-position in an acceptor, which may be glucose or (1,4)-alpha-D-glucan.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     transferase activity     3 terms  

 

 
DOI no: 10.1074/jbc.M701444200 J Biol Chem 282:17242-17249 (2007)
PubMed id: 17420245  
 
 
Three-way stabilization of the covalent intermediate in amylomaltase, an alpha-amylase-like transglycosylase.
T.R.Barends, J.B.Bultema, T.Kaper, M.J.van der Maarel, L.Dijkhuizen, B.W.Dijkstra.
 
  ABSTRACT  
 
Amylomaltases are glycosyl hydrolases belonging to glycoside hydrolase family 77 that are capable of the synthesis of large cyclic glucans and the disproportionation of oligosaccharides. Using protein crystallography, we have generated a flip-book movie of the amylomaltase catalytic cycle in atomic detail. The structures include a covalent glycosyl-enzyme intermediate, and a covalent intermediate in complex with an analogue of a co-substrate, and show how the structures of both enzyme and substrate respond to the changes required by the catalytic cycle as it proceeds. Notably, the catalytic nucleophile changes conformation dramatically during the reaction. Also, Gln256 on the 250s loop is involved in orienting the substrate in the +1 site. The absence of a suitable base in the covalent intermediate structure explains the low hydrolysis activity.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Crystallographic analysis of amylomaltase complexes. A, stereo figure of the F[o] - DF[c] electron density for acarbose bound to Asp-293, calculated prior to incorporation of acarbose in the model. The density was contoured at 2.5 and overlaid on the refined structure. B, F[o] - DF[c] electron density after refinement with a non-covalently bound acarbose. To check the density for the covalent bond and to correctly identify the various acarbose residues, the Asp-293 carboxylate group as well as the acarbose 6-OH groups were omitted from the calculations (see "Materials and Methods"). Positive difference density is shown in green (3.5 ), negative density in red (-3.5 ). 2mF[o] - DF[c] density (blue, 1.0 ) (C) F[o] - DF[c] electron density (green, 2.5 ) (D) for the covalent intermediate-4-deoxyglucose complex. To avoid model bias, both maps were calculated prior to the incorporation of 4-deoxyglucose in the model. All figures were produced using PyMol (37).
Figure 4.
FIGURE 4. Stereo images of structures representing different states during the reaction cycle of amylomaltase. A, empty active site at pH 5.6. The residues Asp-293, Glu-340, Asp-395, and Gln-256 are indicated. B, acarbose (ACR) complex as determined by Przylas et al. (22). The subsites +1 and -1 are indicated. C, acarbose covalent intermediate-4-deoxyglucose complex. D, covalent intermediate with acarbose. Possible hydrolytic water molecules are indicated as spheres.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 17242-17249) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21117235 J.H.Jung, T.Y.Jung, D.H.Seo, S.M.Yoon, H.C.Choi, B.C.Park, C.S.Park, and E.J.Woo (2011).
Structural and functional analysis of substrate recognition by the 250s loop in amylomaltase from Thermus brockianus.
  Proteins, 79, 633-644.
PDB code: 2x1i
22027553 O.Kartal, S.Mahlow, A.Skupin, and O.Ebenhöh (2011).
Carbohydrate-active enzymes exemplify entropic principles in metabolism.
  Mol Syst Biol, 7, 542.  
19940122 A.I.Guce, N.E.Clark, E.N.Salgado, D.R.Ivanen, A.A.Kulminskaya, H.Brumer, and S.C.Garman (2010).
Catalytic mechanism of human alpha-galactosidase.
  J Biol Chem, 285, 3625-3632.
PDB codes: 3hg2 3hg3 3hg4 3hg5
21118988 A.Vujicic-Zagar, T.Pijning, S.Kralj, C.A.López, W.Eeuwema, L.Dijkhuizen, and B.W.Dijkstra (2010).
Crystal structure of a 117 kDa glucansucrase fragment provides insight into evolution and product specificity of GH70 enzymes.
  Proc Natl Acad Sci U S A, 107, 21406-21411.
PDB codes: 3hz3 3klk 3kll
20159465 N.M.Koropatkin, and T.J.Smith (2010).
SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules.
  Structure, 18, 200-215.
PDB codes: 3k8k 3k8l 3k8m
19367403 R.M.Kelly, L.Dijkhuizen, and H.Leemhuis (2009).
The evolution of cyclodextrin glucanotransferase product specificity.
  Appl Microbiol Biotechnol, 84, 119-133.  
18558099 D.J.Vocadlo, and G.J.Davies (2008).
Mechanistic insights into glycosidase chemistry.
  Curr Opin Chem Biol, 12, 539-555.  
18703518 E.J.Woo, S.Lee, H.Cha, J.T.Park, S.M.Yoon, H.N.Song, and K.H.Park (2008).
Structural insight into the bifunctional mechanism of the glycogen-debranching enzyme TreX from the archaeon Sulfolobus solfataricus.
  J Biol Chem, 283, 28641-28648.
PDB codes: 2vnc 2vr5 2vuy
19016850 S.Kralj, S.S.van Leeuwen, V.Valk, W.Eeuwema, J.P.Kamerling, and L.Dijkhuizen (2008).
Hybrid reuteransucrase enzymes reveal regions important for glucosidic linkage specificity and the transglucosylation/hydrolysis ratio.
  FEBS J, 275, 6002-6010.  
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 code is shown on the right.