3IAI

Crystal structure of the catalytic domain of the tumor-associated human carbonic anhydrase IX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.157 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Crystal structure of the catalytic domain of the tumor-associated human carbonic anhydrase IX.

Alterio, V.Hilvo, M.Di Fiore, A.Supuran, C.T.Pan, P.Parkkila, S.Scaloni, A.Pastorek, J.Pastorekova, S.Pedone, C.Scozzafava, A.Monti, S.M.De Simone, G.

(2009) Proc Natl Acad Sci U S A 106: 16233-16238

  • DOI: 10.1073/pnas.0908301106
  • Primary Citation of Related Structures:  
    3IAI

  • PubMed Abstract: 
  • Carbonic anhydrase (CA) IX is a plasma membrane-associated member of the alpha-CA enzyme family, which is involved in solid tumor acidification. It is a marker of tumor hypoxia and a prognostic factor in several human cancers. An aberrant increase in CA IX expression in chronic hypoxia and during development of various carcinomas contributes to tumorigenesis through at least two mechanisms: pH regulation and cell adhesion control ...

    Carbonic anhydrase (CA) IX is a plasma membrane-associated member of the alpha-CA enzyme family, which is involved in solid tumor acidification. It is a marker of tumor hypoxia and a prognostic factor in several human cancers. An aberrant increase in CA IX expression in chronic hypoxia and during development of various carcinomas contributes to tumorigenesis through at least two mechanisms: pH regulation and cell adhesion control. Here we report the X-ray structure of the catalytic domain of CA IX in complex with a classical, clinically used sulfonamide inhibitor, acetazolamide. The structure reveals a typical alpha-CA fold, which significantly differs from the other CA isozymes when the protein quaternary structure is considered. Thus, two catalytic domains of CA IX associate to form a dimer, which is stabilized by the formation of an intermolecular disulfide bond. The active site clefts and the PG domains are located on one face of the dimer, while the C-termini are located on the opposite face to facilitate protein anchoring to the cell membrane. A correlation between the three-dimensional structure and the physiological role of the enzyme is here suggested, based on the measurement of the pH profile of the catalytic activity for the physiological reaction, CO(2) hydration to bicarbonate and protons. On the basis of the structural differences observed between CA IX and the other membrane-associated alpha-CAs, further prospects for the rational drug design of isozyme-specific CA inhibitors are proposed, given that inhibition of this enzyme shows antitumor activity both in vitro and in vivo.


    Organizational Affiliation

    Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Naples, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbonic anhydrase 9A, B, C, D257Homo sapiensMutation(s): 1 
Gene Names: CA9G250MN
EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16790 (Homo sapiens)
Explore Q16790 
Go to UniProtKB:  Q16790
PHAROS:  Q16790
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE, F, G, H5N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G22768VO
GlyCosmos:  G22768VO
GlyGen:  G22768VO
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AZM
Query on AZM

Download Ideal Coordinates CCD File 
FA [auth C], J [auth A], OA [auth D], V [auth B]5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE
C4 H6 N4 O3 S2
BZKPWHYZMXOIDC-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download Ideal Coordinates CCD File 
CA [auth B], LA [auth C], R [auth A], WA [auth D]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
DA [auth B], MA [auth C], S [auth A], T [auth A], XA [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , GA [auth C] , HA [auth C] , IA [auth C] , JA [auth C] , K [auth A] , KA [auth C] , 
AA [auth B],  BA [auth B],  GA [auth C],  HA [auth C],  IA [auth C],  JA [auth C],  K [auth A],  KA [auth C],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  PA [auth D],  Q [auth A],  QA [auth D],  RA [auth D],  SA [auth D],  TA [auth D],  UA [auth D],  VA [auth D],  W [auth B],  X [auth B],  Y [auth B],  Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
EA [auth C], I [auth A], NA [auth D], U [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AZMKd:  22   nM  BindingDB
AZMKd:  20   nM  BindingDB
AZMIC50:  132   nM  BindingDB
AZMIC50:  42.099998474121094   nM  BindingDB
AZMIC50:  94   nM  BindingDB
AZMKi:  3   nM  BindingDB
AZMKd:  50   nM  BindingDB
AZMIC50:  82   nM  BindingDB
AZMIC50:  123.5999984741211   nM  BindingDB
AZMIC50:  73   nM  BindingDB
AZMIC50:  71   nM  BindingDB
AZMIC50:  304.6000061035156   nM  BindingDB
AZMIC50:  318.6000061035156   nM  BindingDB
AZMIC50:  52.5   nM  BindingDB
AZMIC50:  54   nM  BindingDB
AZMIC50:  746.9000244140625   nM  BindingDB
AZMIC50:  32   nM  BindingDB
AZMKi:  0.05999999865889549   nM  BindingDB
AZMKd:  8.5   nM  BindingDB
AZMIC50:  30   nM  BindingDB
AZMKi:  0.800000011920929   nM  BindingDB
AZMIC50:  65.19999694824219   nM  BindingDB
AZMIC50:  28   nM  BindingDB
AZMIC50:  243.10000610351562   nM  BindingDB
AZMIC50:  27   nM  BindingDB
AZMIC50:  236.10000610351562   nM  BindingDB
AZMIC50:  21   nM  BindingDB
AZMKd:  14   nM  BindingDB
AZMIC50:  44.29999923706055   nM  BindingDB
AZMKi:  20   nM  BindingDB
PO4Ki:  560000   nM  BindingDB
AZMIC50:  48.70000076293945   nM  BindingDB
AZMKi:  5.599999904632568   nM  BindingDB
AZMKi:  25   nM  BindingDB
AZMIC50:  410.29998779296875   nM  BindingDB
AZMIC50:  999.7999877929688   nM  BindingDB
AZMKi:  26   nM  BindingDB
AZMKi:  30   nM  BindingDB
AZMIC50:  2134   nM  BindingDB
AZMIC50:  36.20000076293945   nM  BindingDB
AZMIC50:  1997   nM  BindingDB
AZMIC50:  36.70000076293945   nM  BindingDB
AZMIC50:  200.60000610351562   nM  BindingDB
AZMIC50:  208.10000610351562   nM  BindingDB
AZMIC50:  1764   nM  BindingDB
AZMIC50:  2.5999999046325684   nM  BindingDB
AZMIC50:  1513   nM  BindingDB
AZMIC50:  1520   nM  BindingDB
AZMIC50:  1524   nM  BindingDB
AZMKd:  3   nM  BindingDB
AZMIC50:  1297   nM  BindingDB
AZMIC50:  1294   nM  BindingDB
AZMIC50:  1165   nM  BindingDB
AZMIC50:  1024   nM  BindingDB
AZMIC50:  973   nM  BindingDB
AZMIC50:  903   nM  BindingDB
AZMIC50:  174.8000030517578   nM  BindingDB
AZMIC50:  176.8000030517578   nM  BindingDB
AZMIC50:  183.3000030517578   nM  BindingDB
AZMIC50:  763   nM  BindingDB
AZMIC50:  775   nM  BindingDB
AZMIC50:  721   nM  BindingDB
AZMIC50:  735   nM  BindingDB
AZMIC50:  680   nM  BindingDB
AZMIC50:  694.5   nM  BindingDB
AZMIC50:  700   nM  BindingDB
AZMIC50:  218.8000030517578   nM  BindingDB
AZMKd:  6.699999809265137   nM  BindingDB
AZMIC50:  622   nM  BindingDB
AZMIC50:  53.400001525878906   nM  BindingDB
AZMKi:  9   nM  BindingDB
AZMIC50:  440   nM  BindingDB
AZMKd:  5   nM  BindingDB
AZMIC50:  56.70000076293945   nM  BindingDB
AZMKd:  0.029999999329447746   nM  BindingDB
AZMIC50:  7.699999809265137   nM  BindingDB
AZMIC50:  286.5   nM  BindingDB
AZMKi:  16   nM  BindingDB
AZMIC50:  670.2999877929688   nM  BindingDB
AZMKd:  1   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.157 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.18α = 90
b = 144.18β = 90
c = 208.89γ = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary