Primary Citation PubMed: 10747009
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Structural insights into the substrate tunnel of Saccharomyces cerevisiae carbonic anhydrase Nce103.
(2009) BMC Struct Biol 9
PubMed: 19852838 | PubMedCentral: PMC2775743 | DOI: 10.1186/1472-6807-9-67
The structure of Nce103ΔN13 resembles that of other plant type β-class CAs ( P. sativum , PDB code: 1ekj [ 11 ]; P. purpureum , PDB code: 1ddz [ 12 ]; E. coli , PDB codes: 1i6p [ 3 ] a... d 1t75 ; H. influenzae , PDB code: 2a8c [ 5 ]; M. tuberculosis Rv3588c, PDB codes: 1ym3 [ 13 ] and 2a5v [ 14 ], C. neoformans , PDB codes: 2w3n and 2w3q [ 15 ]).
Comparison between the active sites of Nce103 and β-CAs from other species The crystal structure of Nce103 was superimposed on three β-CA homologs from P. sativum (PSCA; PDB code: 1ekj ), E. coli (ECCA; PDB code: 2esf ) and C. neoformans (Can2; PDB code: 2w3n ), giving a root mean squared deviation (RMSD) of 1.58 Å, 1.96 Å and 1.95 Å, respectively, for 197 Cα-atoms.
Publication Year: 2009
FragKB: structural and literature annotation resource of conserved peptide fragments and residues.
(2010) PLoS One 5
PubMed: 20305778 | PubMedCentral: PMC2841175 | DOI: 10.1371/journal.pone.0009679
Carbonic anhydrase from P. sativum (PDB: 1EKJ); the fragment includes the conserved Gln 61; this residue is regarded as catalytic in homologous proteins.
Publication Year: 2010
Structural studies of ?-carbonic anhydrase from the green alga Coccomyxa: inhibitor complexes with anions and acetazolamide.
(2011) PLoS One 6
PubMed: 22162771 | PubMedCentral: PMC3230598 | DOI: 10.1371/journal.pone.0028458
Previously determined structures of β-CAs are available from six different organisms including higher plants: Pisum sativum (pea) ( Ps -CA, pdb code 1EKJ,  ); microalgae P. purpureum ( Pp ... CA, pdb code 1DDZ,  ); bacteria including E. coli ( Ec -CA, pdb code 1I6P  ), Mycobacterium tuberculosis ( Mt -CA, pdb code 1YLK  ) and Haemophilus influenzae ( Hi -CA, pdb code 2A8D  ); the chemoautotroph Halothiobacillus neapolitanus (pdb code 2FGY  ), and the “cab”-type β-CA from the thermophilic archaeon Methanobacteriumthermoautotrophicum (pdb code 1G5C  ).
The Co -CA-AZM structure was solved by molecular replacement (MR) using the program CNS  and the Ps -CA structure, pdb code 1EKJ  asa search model.
Publication Year: 2011
Beta carbonic anhydrases: novel targets for pesticides and anti-parasitic agents in agriculture and livestock husbandry.
(2014) Parasit Vectors 7
PubMed: 25174433 | PubMedCentral: PMC4162934 | DOI: 10.1186/1756-3305-7-403
Two residues in PDB model 1EKJ (β-CA from Pisum sativum ) appear considerably smaller than their complements in the Ancylostoma caninum -based homology model, and those residues can be conside... ed to be only partially exposed (Figure 4 , indicated by yellow colour in the alignment).
The structural availability of the epitope in the PDB model 1EKJ (β-CA from Pisum sativum ) and the homology model based on the β-CA sequence from Ancylostoma caninum was studied by preparing the molecular surface with VMD, using a probe radius of 1.4 Å.
An alignment containing PDB 1EKJ and the corresponding sequence from Ancylostoma caninum predicted β-CA is shown.
(A) Cartoon presentation of β-CA from Pisum sativum (PDB 1EKJ).
Results for three out of these four searches revealed that PDB structure 1EKJ (β-CA from Pisum sativum ) possessed the most similar sequence, while PDB id 2A5V (β-CA from Mycobacterium tuberculosis ) was found to be the most similar to C4LXK3 ( Entamoeba histolytica ).
(C) Aligned homology models of β-CAs from Ancylostoma caninum (green), Ascaris suum (blue), and Trichinella spiralis (orange) are shown with PDB 1EKJ (gray).
Homology modelling was performed according to multiple sequence alignment containing FC551456 ( Ancylostoma caninum ), F1LE18 ( Ascaris suum ), E5SH53 ( Trichinella spiralis ), and PDB 1EKJ by using the Modeller program (version 9.13) [ 57 ] with PDB model 1EKJ (β-CA from Pisum sativum ) as a template.
To study the molecular availability of the predicted main antigenic epitope, surface exposure of the homology model created from PDB model 1EKJ (β-CA from Pisum sativum ) and the homology model based on the β-CA sequence from Ancylostoma caninum were studied by visualizing the molecular surface (Figure 4 ).
Publication Year: 2014
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