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PDBsum entry 1kxt

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protein metals Protein-protein interface(s) links
Hydrolase, immune system PDB id
1kxt
Jmol
Contents
Protein chains
496 a.a. *
123 a.a. *
Metals
_CL ×3
_CA ×3
Waters ×1727
* Residue conservation analysis
PDB id:
1kxt
Name: Hydrolase, immune system
Title: Camelid vhh domains in complex with porcine pancreatic alpha-amylase
Structure: Alpha-amylase, pancreatic. Chain: a, c, e. Synonym: 1,4-alpha-d-glucan glucanohydrolase. Immunoglobulin vhh fragment. Chain: b, d, f. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823. Other_details: pancreatic enzyme. Camelus dromedarius. Arabian camel. Organism_taxid: 9838. Gene: igg vhh. Expressed in: escherichia coli.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.203     R-free:   0.236
Authors: A.Desmyter,S.Spinelli,F.Payan,M.Lauwereys,L.Wyns, S.Muyldermans,C.Cambillau
Key ref:
A.Desmyter et al. (2002). Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology. J Biol Chem, 277, 23645-23650. PubMed id: 11960990 DOI: 10.1074/jbc.M202327200
Date:
01-Feb-02     Release date:   19-Jun-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00690  (AMYP_PIG) -  Pancreatic alpha-amylase
Seq:
Struc:
511 a.a.
496 a.a.*
Protein chains
No UniProt id for this chain
Struc: 123 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains A, C, E: E.C.3.2.1.1  - Alpha-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
DOI no: 10.1074/jbc.M202327200 J Biol Chem 277:23645-23650 (2002)
PubMed id: 11960990  
 
 
Three camelid VHH domains in complex with porcine pancreatic alpha-amylase. Inhibition and versatility of binding topology.
A.Desmyter, S.Spinelli, F.Payan, M.Lauwereys, L.Wyns, S.Muyldermans, C.Cambillau.
 
  ABSTRACT  
 
Camelids produce functional antibodies devoid of light chains and CH1 domains. The antigen-binding fragment of such heavy chain antibodies is therefore comprised in one single domain, the camelid heavy chain antibody VH (VHH). Here we report on the structures of three dromedary VHH domains in complex with porcine pancreatic alpha-amylase. Two VHHs bound outside the catalytic site and did not inhibit or inhibited only partially the amylase activity. The third one, AMD9, interacted with the active site crevice and was a strong amylase inhibitor (K(i) = 10 nm). In contrast with complexes of other proteinaceous amylase inhibitors, amylase kept its native structure. The water-accessible surface areas of VHHs covered by amylase ranged between 850 and 1150 A(2), values similar to or even larger than those observed in the complexes between proteins and classical antibodies. These values could certainly be reached because a surprisingly high extent of framework residues are involved in the interactions of VHHs with amylase. The framework residues that participate in the antigen recognition represented 25-40% of the buried surface. The inhibitory interaction of AMD9 involved mainly its complementarity-determining region (CDR) 2 loop, whereas the CDR3 loop was small and certainly did not protrude as it does in cAb-Lys3, a VHH-inhibiting lysozyme. AMD9 inhibited amylase, although it was outside the direct reach of the catalytic residues; therefore it is to be expected that inhibiting VHHs might also be elicited against proteases. These results illustrate the versatility and efficiency of VHH domains as protein binders and enzyme inhibitors and are arguments in favor of their use as drugs against diabetes.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Sequences and three-dimensional structures of the three VHHs. The three CDRs (1-3) are colored red, green, and blue, respectively, and the cysteines are purple. A, anti-PPA AMB7, AMD9, and AMD10 VHH amino acid sequences. The numbering is according to Kabat ( 30). B, from left to right, views of the AMB7, AMD9, and AMD10 VHHs in the same orientation with the CDR3 oriented in front (view made with SPOCK (33)).
Figure 2.
Fig. 2. Views of the three VHHs superimposed on PPA with the acarbose molecule bound (pink). The PPA surface is in gray, and its visible catalytic residue Asp-300 is in red. The C trace of the VHHs is orange, the three CDRs (1-3) are colored red, green, and blue, respectively, and each VHH surface is transparent. Inset, close-up view of the PPA active site with the inhibitory AMD9 VHH bound. The saccharidic inhibitor acarbose has been positioned in the active site according to the x-ray structure as a probe of the saccharide position. Two residues of the VHH, Tyr-52 and Arg-52a (CPK yellow and orange), clash with the modeled acarbose (views made with SPOCK (33)).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 23645-23650) copyright 2002.  

Literature references that cite this PDB file's key reference

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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.