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PDBsum entry 3k1d

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protein links
Transferase PDB id
3k1d
Jmol
Contents
Protein chain
722 a.a. *
Waters ×323
* Residue conservation analysis
PDB id:
3k1d
Name: Transferase
Title: Crystal structure of glycogen branching enzyme synonym: 1,4- glucan:1,4-alpha-d-glucan 6-glucosyl-transferase from mycob tuberculosis h37rv
Structure: 1,4-alpha-glucan-branching enzyme. Chain: a. Fragment: residues 10-731. Synonym: glycogen-branching enzyme, be, 1,4-alpha-d-glucan: d-glucan 6-glucosyl-transferase. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 83332. Strain: h37rv. Gene: glgb, rv1326c. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.33Å     R-factor:   0.193     R-free:   0.236
Authors: K.Pal,S.Kumar,K.Swaminathan
Key ref: K.Pal et al. (2010). Crystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity. J Biol Chem, 285, 20897-20903. PubMed id: 20444687
Date:
27-Sep-09     Release date:   05-May-10    
PROCHECK
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 Headers
 References

Protein chain
Pfam  
P9WN44  (GLGB_MYCTO) -  1,4-alpha-glucan branching enzyme GlgB
Seq:
Struc:
 
Seq:
Struc:
731 a.a.
722 a.a.*
Protein chain
Pfam  
P9WN45  (GLGB_MYCTU) -  1,4-alpha-glucan branching enzyme GlgB
Seq:
Struc:
 
Seq:
Struc:
731 a.a.
722 a.a.
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.2.4.1.18  - 1,4-alpha-glucan branching enzyme.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Formation of 1,6-glucosidic linkages of glycogen.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     carbohydrate metabolic process   4 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
J Biol Chem 285:20897-20903 (2010)
PubMed id: 20444687  
 
 
Crystal structure of full-length Mycobacterium tuberculosis H37Rv glycogen branching enzyme: insights of N-terminal beta-sandwich in substrate specificity and enzymatic activity.
K.Pal, S.Kumar, S.Sharma, S.K.Garg, M.S.Alam, H.E.Xu, P.Agrawal, K.Swaminathan.
 
  ABSTRACT  
 
The open reading frame Rv1326c of Mycobacterium tuberculosis (Mtb) H37Rv encodes for an alpha-1,4-glucan branching enzyme (MtbGlgB, EC 2.4.1.18, Uniprot entry Q10625). This enzyme belongs to glycoside hydrolase (GH) family 13 and catalyzes the branching of a linear glucose chain during glycogenesis by cleaving a 1-->4 bond and making a new 1-->6 bond. Here, we show the crystal structure of full-length MtbGlgB (MtbGlgBWT) at 2.33-A resolution. MtbGlgBWT contains four domains: N1 beta-sandwich, N2 beta-sandwich, a central (beta/alpha)(8) domain that houses the catalytic site, and a C-terminal beta-sandwich. We have assayed the amylase activity with amylose and starch as substrates and the glycogen branching activity using amylose as a substrate for MtbGlgBWT and the N1 domain-deleted (the first 108 residues deleted) MtbDelta108GlgB protein. The N1 beta-sandwich, which is formed by the first 105 amino acids and superimposes well with the N2 beta-sandwich, is shown to have an influence in substrate binding in the amylase assay. Also, we have checked and shown that several GH13 family inhibitors are ineffective against MtbGlgBWT and MtbDelta108GlgB. We propose a two-step reaction mechanism, for the amylase activity (1-->4 bond breakage) and isomerization (1-->6 bond formation), which occurs in the same catalytic pocket. The structural and functional properties of MtbGlgB and MtbDelta108GlgB are compared with those of the N-terminal 112-amino acid-deleted Escherichia coli GlgB (ECDelta112GlgB).