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PDBsum entry 3d0n

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protein ligands metals Protein-protein interface(s) links
Metal binding protein PDB id
3d0n
Jmol
Contents
Protein chain
263 a.a. *
Ligands
ACT ×2
GOL
Metals
_ZN ×2
Waters ×777
* Residue conservation analysis
PDB id:
3d0n
Name: Metal binding protein
Title: Crystal structure of human carbonic anhydrase xiii
Structure: Carbonic anhydrase 13. Chain: a, b. Synonym: carbonic anhydrase xiii, carbonate dehydratase xii xiii. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: ca13. Expressed in: escherichia coli.
Resolution:
1.55Å     R-factor:   0.168     R-free:   0.188
Authors: A.Di Fiore,G.De Simone
Key ref:
A.Di Fiore et al. (2008). Crystal structure of human carbonic anhydrase XIII and its complex with the inhibitor acetazolamide. Proteins, 74, 164-175. PubMed id: 18618712 DOI: 10.1002/prot.22144
Date:
02-May-08     Release date:   29-Jul-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8N1Q1  (CAH13_HUMAN) -  Carbonic anhydrase 13
Seq:
Struc:
262 a.a.
263 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.1  - Carbonate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: H2CO3 = CO2 + H2O
H(2)CO(3)
=
CO(2)
Bound ligand (Het Group name = ACT)
matches with 75.00% similarity
+ H(2)O
      Cofactor: Zinc
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytosol   1 term 
  Biological process     small molecule metabolic process   3 terms 
  Biochemical function     lyase activity     4 terms  

 

 
    Added reference    
 
 
DOI no: 10.1002/prot.22144 Proteins 74:164-175 (2008)
PubMed id: 18618712  
 
 
Crystal structure of human carbonic anhydrase XIII and its complex with the inhibitor acetazolamide.
A.Di Fiore, S.M.Monti, M.Hilvo, S.Parkkila, V.Romano, A.Scaloni, C.Pedone, A.Scozzafava, C.T.Supuran, G.De Simone.
 
  ABSTRACT  
 
The cytosolic isoform XIII is a recently discovered member of the human carbonic anhydrase (hCA, EC 4.2.1.1) family. It is selectively expressed among other tissues in the reproductive organs, where it may control pH and ion balance regulation, ensuring thus proper fertilization conditions. The authors report here the X-ray crystallographic structure of this isozyme in the unbound state and in complex with a classical sulfonamide inhibitor, namely acetazolamide. A detailed comparison of the obtained structural data with those already reported for other CA isozymes provides novel insights into the catalytic properties of the members of this protein family. On the basis of the inhibitory properties of acetazolamide against various cytosolic/transmembrane isoforms and the structural differences detected within the active site of the various CA isoforms, further prospects for the design of isozyme-specific CA inhibitors are here proposed. Proteins 2009. (c) 2008 Wiley-Liss, Inc.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Superposition of the hCA XIII (red) and hCA II (green) C trace. The zinc ion and its three histidine ligands are represented in ball and stick.
Figure 6.
Figure 6. Schematic view of the hCA II (A) (PDB code 1CA2),[27] hCA I (B) (PDB code 2CAB),[28] hCA XIII (C), and hCA III (D) (PDB code 1Z93)[26] structures. The zinc ion and its three histidine ligands (H94, H96, and H119) are shown. For each isozyme, the histidine residues participating to the proton-transfer reaction are also reported by PyMOL sphere representation (http://pymol.sourceforge.net/).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2008, 74, 164-175) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21402476 F.Carta, A.Innocenti, R.A.Hall, F.A.Mühlschlegel, A.Scozzafava, and C.T.Supuran (2011).
Carbonic anhydrase inhibitors. Inhibition of the β-class enzymes from the fungal pathogens Candida albicans and Cryptococcus neoformans with branched aliphatic/aromatic carboxylates and their derivatives.
  Bioorg Med Chem Lett, 21, 2521-2526.  
20505865 V.Alterio, S.M.Monti, E.Truppo, C.Pedone, C.T.Supuran, and G.De Simone (2010).
The first example of a significant active site conformational rearrangement in a carbonic anhydrase-inhibitor adduct: the carbonic anhydrase I-topiramate complex.
  Org Biomol Chem, 8, 3528-3533.
PDB code: 3lxe
19805286 V.Alterio, M.Hilvo, A.Di Fiore, C.T.Supuran, P.Pan, S.Parkkila, A.Scaloni, J.Pastorek, S.Pastorekova, C.Pedone, A.Scozzafava, S.M.Monti, and G.De Simone (2009).
Crystal structure of the catalytic domain of the tumor-associated human carbonic anhydrase IX.
  Proc Natl Acad Sci U S A, 106, 16233-16238.
PDB code: 3iai
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 code is shown on the right.