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. 2004 Sep 9;101(38):13726–13731. doi: 10.1073/pnas.0405082101

Fig. 2.

Fig. 2.

Sequence alignment of NfdA with distantly related proteins. Each region of the amino acid sequences of cytosine deaminase (CodA), dihydroorotase (PyrC), and urease α-subunit (UreC) contains a β-strand secondary structure in which the functional residues (histidine and aspartic acid) map to the C terminus of strands 1, 5, 6, and 8 in each enzyme (30). For NfdA, LAF3–1, HutI, and AtzA, the regions containing the predicted secondary structures that correspond to β1, 5, 6, or 8 of CodA, PyrC, and UreC are shown. LAF3 isoform 1 (LAF3–1) is from A. thaliana (GenBank accession no. AAP55749), AepA precursor (AepA) is from B. melitensis 16M (GenBank accession no. NP_541100.1), imidazolonepropionase (HutI) is from Caulobacter crescentus (SwissProt accession no. P58079), atrazine chlorohydrolase (AtzA) is from Pseudomonas sp. ADP (SwissProt accession no. P72156), cytosine deaminase (CodA) is from E. coli (SwissProt accession no. P25524), dihydroorotase (PyrC) is from E. coli (SwissProt accession no. P05020), and urease α-subunit (UreC) is from Klebsiella aerogenes (SwissProt accession no. P18314). The residues with amino acid numbers and vertical arrows are metal ligands established by x-ray crystallography of CodA (PDB ID code 1K6W), PyrC (PDB ID code 1J79), UreC (PDB ID code 2KAU), and the corresponding residues in the other proteins. The residues highlighted in reverse type are conserved in NfdA and all of the other proteins. Except for the residues highlighted in reverse type, identical amino acid residues in either of the regulatory proteins and the members of the amidohydrolase superfamily are boxed.