PDBsum entry 1m7x

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Transferase PDB id
Protein chains
587 a.a. *
Waters ×1142
* Residue conservation analysis
PDB id:
Name: Transferase
Title: The x-ray crystallographic structure of branching enzyme
Structure: 1,4-alpha-glucan branching enzyme. Chain: a, b, c, d. Fragment: residues 113-728. Synonym: glycogen branching enzyme. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.30Å     R-factor:   0.200     R-free:   0.265
Authors: M.C.Abad,K.Binderup,J.Rios-Steiner,R.K.Arni,J.Preiss, J.H.Geiger
Key ref:
M.C.Abad et al. (2002). The X-ray crystallographic structure of Escherichia coli branching enzyme. J Biol Chem, 277, 42164-42170. PubMed id: 12196524 DOI: 10.1074/jbc.M205746200
23-Jul-02     Release date:   18-Sep-02    
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Protein chains
Pfam   ArchSchema ?
P07762  (GLGB_ECOLI) -  1,4-alpha-glucan branching enzyme GlgB
728 a.a.
587 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   2 terms 
  Biochemical function     catalytic activity     4 terms  


DOI no: 10.1074/jbc.M205746200 J Biol Chem 277:42164-42170 (2002)
PubMed id: 12196524  
The X-ray crystallographic structure of Escherichia coli branching enzyme.
M.C.Abad, K.Binderup, J.Rios-Steiner, R.K.Arni, J.Preiss, J.H.Geiger.
Branching enzyme catalyzes the formation of alpha-1,6 branch points in either glycogen or starch. We report the 2.3-A crystal structure of glycogen branching enzyme from Escherichia coli. The enzyme consists of three major domains, an NH(2)-terminal seven-stranded beta-sandwich domain, a COOH-terminal domain, and a central alpha/beta-barrel domain containing the enzyme active site. While the central domain is similar to that of all the other amylase family enzymes, branching enzyme shares the structure of all three domains only with isoamylase. Oligosaccharide binding was modeled for branching enzyme using the enzyme-oligosaccharide complex structures of various alpha-amylases and cyclodextrin glucanotransferase and residues were implicated in oligosaccharide binding. While most of the oligosaccharides modeled well in the branching enzyme structure, an approximate 50 degrees rotation between two of the glucose units was required to avoid steric clashes with Trp(298) of branching enzyme. A similar rotation was observed in the mammalian alpha-amylase structure caused by an equivalent tryptophan residue in this structure. It appears that there are two binding modes for oligosaccharides in these structures depending on the identity and location of this aromatic residue.
  Selected figure(s)  
Figure 2.
Fig. 2. Ribbon depiction of the x-ray crystal structure of E. coli BE truncated at amino acid 113. Residues involved in BE catalysis are shown in green, with atoms colored by type: red, oxygen; green, carbon; blue, nitrogen. Red indicates the NH[2]-terminal domain; orange indicates the central / barrel catalytic domain; and blue indicates the COOH-terminal domain. This and all other depictions of the structure were made using RIBBONS (39).
Figure 6.
Fig. 6. Electrostatic potential surface picture of BE looking down the barrel (a) and rotated 180^o (b). The EPS calculation corresponds to 10 kT/e for the blue color, 10 kT/e for red, and an EPS ~0 is white, where 10 kT ~6 kcal/mol. EPS calculation and figure were made using GRASP (40).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 42164-42170) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21104698 C.R.Santos, C.C.Tonoli, D.M.Trindade, C.Betzel, H.Takata, T.Kuriki, T.Kanai, T.Imanaka, R.K.Arni, and M.T.Murakami (2011).
Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.
  Proteins, 79, 547-557.
PDB codes: 3n8t 3n92 3n98
20360021 R.Matsushima, M.Maekawa, N.Fujita, and W.Sakamoto (2010).
A rapid, direct observation method to isolate mutants with defects in starch grain morphology in rice.
  Plant Cell Physiol, 51, 728-741.  
19244233 F.Sheng, X.Jia, A.Yep, J.Preiss, and J.H.Geiger (2009).
The crystal structures of the open and catalytically competent closed conformation of Escherichia coli glycogen synthase.
  J Biol Chem, 284, 17796-17807.
PDB codes: 2qzs 2r4t 2r4u 3cop 3d1j 3guh
19139240 M.Palomo, S.Kralj, M.J.van der Maarel, and L.Dijkhuizen (2009).
The unique branching patterns of Deinococcus glycogen branching enzymes are determined by their N-terminal domains.
  Appl Environ Microbiol, 75, 1355-1362.  
19121228 S.K.Garg, M.S.Alam, R.Bajpai, K.R.Kishan, and P.Agrawal (2009).
Redox Biology of Mycobacterium tuberculosis H37Rv: protein-protein interaction between GlgB and WhiB1 involves exchange of thiol-disulfide.
  BMC Biochem, 10, 1.  
19897896 T.Akasaka, N.T.Vu, K.Chaen, A.Nishi, H.Satoh, H.Ida, T.Omori, and M.Kimura (2009).
The action of rice branching enzyme I (BEI) on starches.
  Biosci Biotechnol Biochem, 73, 2516-2518.  
16885460 T.Murakami, T.Kanai, H.Takata, T.Kuriki, and T.Imanaka (2006).
A novel branching enzyme of the GH-57 family in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1.
  J Bacteriol, 188, 5915-5924.  
16216577 G.Polekhina, A.Gupta, B.J.van Denderen, S.C.Feil, B.E.Kemp, D.Stapleton, and M.W.Parker (2005).
Structural basis for glycogen recognition by AMP-activated protein kinase.
  Structure, 13, 1453-1462.
PDB codes: 1z0m 1z0n
15272305 A.Buschiazzo, J.E.Ugalde, M.E.Guerin, W.Shepard, R.A.Ugalde, and P.M.Alzari (2004).
Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation.
  EMBO J, 23, 3196-3205.
PDB codes: 1rzu 1rzv
15003223 S.Jobling (2004).
Improving starch for food and industrial applications.
  Curr Opin Plant Biol, 7, 210-218.  
12747837 G.Polekhina, A.Gupta, B.J.Michell, B.van Denderen, S.Murthy, S.C.Feil, I.G.Jennings, D.J.Campbell, L.A.Witters, M.W.Parker, B.E.Kemp, and D.Stapleton (2003).
AMPK beta subunit targets metabolic stress sensing to glycogen.
  Curr Biol, 13, 867-871.  
12581203 S.Janecek, B.Svensson, and E.A.MacGregor (2003).
Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.
  Eur J Biochem, 270, 635-645.  
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.