PDBsum entry 1jib

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Hydrolase PDB id
Jmol PyMol
Protein chains
585 a.a. *
MTT ×2
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Complex of alpha-amylase ii (tva ii) from thermoactinomyces vulgaris r-47 with maltotetraose based on a crystal soaked with maltohexaose.
Structure: Neopullulanase. Chain: a, b. Engineered: yes. Mutation: yes
Source: Thermoactinomyces vulgaris. Organism_taxid: 2026. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
3.30Å     R-factor:   0.212     R-free:   0.304
Authors: T.Yokota,T.Tonozuka,Y.Shimura,K.Ichikawa,S.Kamitori,Y.Sakano
Key ref: T.Yokota et al. (2001). Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues. Biosci Biotechnol Biochem, 65, 619-626. PubMed id: 11330677
02-Jul-01     Release date:   25-Jul-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q08751  (NEPU2_THEVU) -  Neopullulanase 2
585 a.a.
585 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.  - Neopullulanase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of pullulan to panose (6-alpha-D-glucosylmaltose).
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     6 terms  


Biosci Biotechnol Biochem 65:619-626 (2001)
PubMed id: 11330677  
Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues.
T.Yokota, T.Tonozuka, Y.Shimura, K.Ichikawa, S.Kamitori, Y.Sakano.
The structures of Thermoactinomyces vulgaris R-47 alpha-amylase II mutant (d325nTVA II) complexed with substrate analogues, methyl beta-cyclodextrin (m beta-CD) and maltohexaose (G6), were solved by X-ray diffraction at 3.2 A and 3.3 A resolution, respectively. In d325nTVA II-m beta-CD complex, the orientation and binding-position of beta-CD in TVA II were identical to those in cyclodextin glucanotransferase (CGTase). The active site residues were essentialy conserved, while there are no residues corresponding to Tyr89, Phe183, and His233 of CGTase in TVA II. In d325nTVA II-G6 complex, the electron density maps of two glucosyl units at the non-reducing end were disordered and invisible. The four glucosyl units of G6 were bound to TVA II as in CGTase, while the others were not stacked and were probably flexible. The residues of TVA II corresponding to Tyr89, Lys232, and His233 of CGTase were completely lacking. These results suggest that the lack of the residues related to alpha-glucan and CD-stacking causes the functional distinctions between CGTase and TVA II.

Literature references that cite this PDB file's key reference

  PubMed id Reference
15182368 M.Mizuno, T.Tonozuka, A.Uechi, A.Ohtaki, K.Ichikawa, S.Kamitori, A.Nishikawa, and Y.Sakano (2004).
The crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product.
  Eur J Biochem, 271, 2530-2538.
PDB code: 1vb9
12005440 S.C.Garman, L.Hannick, A.Zhu, and D.N.Garboczi (2002).
The 1.9 A structure of alpha-N-acetylgalactosaminidase: molecular basis of glycosidase deficiency diseases.
  Structure, 10, 425-434.
PDB codes: 1ktb 1ktc
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