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PDBsum entry 1g6v

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protein metals Protein-protein interface(s) links
Lyase/immune system PDB id
1g6v
Jmol
Contents
Protein chains
256 a.a. *
126 a.a. *
Metals
_ZN
* Residue conservation analysis
PDB id:
1g6v
Name: Lyase/immune system
Title: Complex of the camelid heavy-chain antibody fragment cab- ca05 with bovine carbonic anhydrase
Structure: Carbonic anhydrase. Chain: a. Antibody heavy chain. Chain: k. Fragment: cab-ca05, variable domain. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Camelus dromedarius. Arabian camel. Organism_taxid: 9838. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Tetramer (from PQS)
Resolution:
3.50Å     R-factor:   0.210     R-free:   0.276
Authors: A.Desmyter,K.Decanniere,S.Muyldermans,L.Wyns
Key ref:
A.Desmyter et al. (2001). Antigen specificity and high affinity binding provided by one single loop of a camel single-domain antibody. J Biol Chem, 276, 26285-26290. PubMed id: 11342547 DOI: 10.1074/jbc.M102107200
Date:
08-Nov-00     Release date:   22-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00921  (CAH2_BOVIN) -  Carbonic anhydrase 2
Seq:
Struc:
260 a.a.
256 a.a.*
Protein chain
No UniProt id for this chain
Struc: 126 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 51 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chain A: E.C.4.2.1.1  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
H(2)CO(3)
= CO(2)
+ H(2)O
      Cofactor: Zn(2+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     plasma membrane   2 terms 
  Biological process     angiotensin-mediated signaling pathway   5 terms 
  Biochemical function     lyase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M102107200 J Biol Chem 276:26285-26290 (2001)
PubMed id: 11342547  
 
 
Antigen specificity and high affinity binding provided by one single loop of a camel single-domain antibody.
A.Desmyter, K.Decanniere, S.Muyldermans, L.Wyns.
 
  ABSTRACT  
 
Detailed knowledge on antibody-antigen recognition is scarce given the unlimited antibody specificities of which only few have been investigated at an atomic level. We report the crystal structures of an antibody fragment derived from a camel heavy chain antibody against carbonic anhydrase, free and in complex with antigen. Surprisingly, this single-domain antibody interacts with nanomolar affinity with the antigen through its third hypervariable loop (19 amino acids long), providing a flat interacting surface of 620 A(2). For the first time, a single-domain antibody is observed with its first hypervariable loop adopting a type-1 canonical structure. The second hypervariable loop, of unique size due to a somatic mutation, reveals a regular beta-turn. The third hypervariable loop covers the remaining hypervariable loops and the side of the domain that normally interacts with the variable domain of the light chain. Specific amino acid substitutions and reoriented side chains reshape this side of the domain and increase its hydrophilicity. Of interest is the substitution of the conserved Trp-103 by Arg because it opens new perspectives to 'humanize' a camel variable domain of heavy chain of heavy chain antibody (VHH) or to 'camelize' a human or a mouse variable domain of heavy chain of conventional antibody (VH).
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Structural organization of the VL-facing side of a VH and its corresponding side in VHHs and a partial camelized human VH. A, VL eye-view of a human VH (1igm, Ref. 50). B, the partial camelized human VH (1vhp, Ref. 36). C, the corresponding side of a VHH, cAb-Lys3 (1mel, Ref. 6) and D, cAb-CA05 (this study). The side chain of residues that take a different conformation among VH and VHH are shown in ball-and-stick and are denoted by their single letter code. The side chains of Arg-38, Tyr-90, and Tyr-91 having similar orientations in VH and VHHs are shown for reference.
Figure 5.
Fig. 5. The antigen-binding site of cAb-CA05. The cAb-CA05 is shown with the scaffold atoms in gray, CDR1 atoms in blue, CDR2 atoms in green. The CDR3 atoms that interact with the antigen are in red for hydrogen bonding, orange for van der Waals contacts, and black for salt bridge. The Kabat numbering of the amino acids to which the contacting atoms belong is given for reference. The carbonic anhydrase epitope segments 1 (pink dots) and 2 (red dots) are in ball-and-stick representation.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 26285-26290) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21244216 F.Rahbarizadeh, D.Ahmadvand, and Z.Sharifzadeh (2011).
Nanobody; an old concept and new vehicle for immunotargeting.
  Immunol Invest, 40, 299-338.  
19955323 L.P.Daley, M.A.Kutzler, B.W.Bennett, M.C.Smith, A.L.Glaser, and J.A.Appleton (2010).
Effector functions of camelid heavy-chain antibodies in immunity to West Nile virus.
  Clin Vaccine Immunol, 17, 239-246.  
20400507 W.W.Koh, S.Steffensen, M.Gonzalez-Pajuelo, B.Hoorelbeke, A.Gorlani, A.Szynol, A.Forsman, M.M.Aasa-Chapman, H.de Haard, T.Verrips, and R.A.Weiss (2010).
Generation of a family-specific phage library of llama single chain antibody fragments that neutralize HIV-1.
  J Biol Chem, 285, 19116-19124.  
19862637 Y.H.Teh, and T.A.Kavanagh (2010).
High-level expression of Camelid nanobodies in Nicotiana benthamiana.
  Transgenic Res, 19, 575-586.  
  19241371 K.Conrath, A.S.Pereira, C.E.Martins, C.G.Timóteo, P.Tavares, S.Spinelli, J.Kinne, C.Flaudrops, C.Cambillau, S.Muyldermans, I.Moura, J.J.Moura, M.Tegoni, and A.Desmyter (2009).
Camelid nanobodies raised against an integral membrane enzyme, nitric oxide reductase.
  Protein Sci, 18, 619-628.  
19033278 M.Arbabi-Ghahroudi, R.To, N.Gaudette, T.Hirama, W.Ding, R.MacKenzie, and J.Tanha (2009).
Aggregation-resistant VHs selected by in vitro evolution tend to have disulfide-bonded loops and acidic isoelectric points.
  Protein Eng Des Sel, 22, 59-66.  
17932913 D.P.Simmons, V.A.Streltsov, O.Dolezal, P.J.Hudson, A.M.Coley, M.Foley, D.F.Proll, and S.D.Nuttall (2008).
Shark IgNAR antibody mimotopes target a murine immunoglobulin through extended CDR3 loop structures.
  Proteins, 71, 119-130.
PDB codes: 2ywy 2ywz
17483488 A.Inoue, S.Y.Sawata, K.Taira, and R.Wadhwa (2007).
Loss-of-function screening by randomized intracellular antibodies: identification of hnRNP-K as a potential target for metastasis.
  Proc Natl Acad Sci U S A, 104, 8983-8988.  
17704915 M.M.Harmsen, and H.J.De Haard (2007).
Properties, production, and applications of camelid single-domain antibody fragments.
  Appl Microbiol Biotechnol, 77, 13-22.  
16358348 A.Marquardt, S.Muyldermans, and M.Przybylski (2006).
A synthetic camel anti-lysozyme peptide antibody (peptibody) with flexible loop structure identified by high-resolution affinity mass spectrometry.
  Chemistry, 12, 1915-1923.  
16537393 E.De Genst, K.Silence, K.Decanniere, K.Conrath, R.Loris, J.Kinne, S.Muyldermans, and L.Wyns (2006).
Molecular basis for the preferential cleft recognition by dromedary heavy-chain antibodies.
  Proc Natl Acad Sci U S A, 103, 4586-4591.
PDB codes: 1zv5 1zvh 1zvy
15640220 E.Dolk, M.van der Vaart, D.Lutje Hulsik, G.Vriend, H.de Haard, S.Spinelli, C.Cambillau, L.Frenken, and T.Verrips (2005).
Isolation of llama antibody fragments for prevention of dandruff by phage display in shampoo.
  Appl Environ Microbiol, 71, 442-450.
PDB code: 1sjx
15753251 L.P.Daley, L.F.Gagliardo, M.S.Duffy, M.C.Smith, and J.A.Appleton (2005).
Application of monoclonal antibodies in functional and comparative investigations of heavy-chain immunoglobulins in new world camelids.
  Clin Diagn Lab Immunol, 12, 380-386.  
15328101 A.Szynol, J.J.de Soet, E.Sieben-van Tuyl, J.W.Bos, and L.G.Frenken (2004).
Bactericidal effects of a fusion protein of llama heavy-chain antibodies coupled to glucose oxidase on oral bacteria.
  Antimicrob Agents Chemother, 48, 3390-3395.  
15130125 E.Veiga, V.de Lorenzo, and L.A.Fernández (2004).
Structural tolerance of bacterial autotransporters for folded passenger protein domains.
  Mol Microbiol, 52, 1069-1080.  
14997552 S.D.Nuttall, K.S.Humberstone, U.V.Krishnan, J.A.Carmichael, L.Doughty, M.Hattarki, A.M.Coley, J.L.Casey, R.F.Anders, M.Foley, R.A.Irving, and P.J.Hudson (2004).
Selection and affinity maturation of IgNAR variable domains targeting Plasmodium falciparum AMA1.
  Proteins, 55, 187-197.  
12662144 C.Souriau, and P.J.Hudson (2003).
Recombinant antibodies for cancer diagnosis and therapy.
  Expert Opin Biol Ther, 3, 305-318.  
12784366 E.Ben-Zeev, A.Berchanski, A.Heifetz, B.Shapira, and M.Eisenstein (2003).
Prediction of the unknown: inspiring experience with the CAPRI experiment.
  Proteins, 52, 41-46.  
12548621 M.K.Fenwick, and F.A.Escobedo (2003).
Hybrid Monte Carlo with multidimensional replica exchanges: conformational equilibria of the hypervariable regions of a llama VHH antibody domain.
  Biopolymers, 68, 160-177.  
12784369 R.Chen, W.Tong, J.Mintseris, L.Li, and Z.Weng (2003).
ZDOCK predictions for the CAPRI challenge.
  Proteins, 52, 68-73.  
12001233 J.G.Renisio, J.Pérez, M.Czisch, M.Guenneugues, O.Bornet, L.Frenken, C.Cambillau, and H.Darbon (2002).
Solution structure and backbone dynamics of an antigen-free heavy chain variable domain (VHH) from Llama.
  Proteins, 47, 546-555.
PDB code: 1g9e
12204693 L.Xu, P.Aha, K.Gu, R.G.Kuimelis, M.Kurz, T.Lam, A.C.Lim, H.Liu, P.A.Lohse, L.Sun, S.Weng, R.W.Wagner, and D.Lipovsek (2002).
Directed evolution of high-affinity antibody mimics using mRNA display.
  Chem Biol, 9, 933-942.  
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.