Figure 4.

Relationship between chorismate mutase domains belonging to the Iα family of cyclohexadienyl mutases. The relationships are shown as a phylogram tree computed with the neighbor-joining method using the Phylo-Win program and multiple alignment input from the ClustalW program. Bootstrap percentages (for 500 iterations) are shown at nodes that define clusters deemed to be significant (above 50%). Accordingly, that portion of the tree where branching order is significant is shown in orange. AroQ, monofunctional chorismate mutase; *AroQ, periplasmic chorismate mutase. A bullet indicates a fusion joint. Thus, AroQPheA indicates an AroQ domain fused at its carboxyl terminus with the amino-terminal portion of a PheA domain. PapB and PchB carry out reactions analogous to chorismate mutase as illustrated in Figure 3. The divergent AroQ protein groupings are highlighted in yellow. Abbreviations for organisms: Actinobacillus actinomycetemcomitans (Aac), Aeropyrum pernix (Ape), Archaeoglobus fulgidus (Afu), Bacillus subtilis (Bsu), Bordetella pertussis (Bpe), Campylobacterium jejeuni (Cje), Chlorobium tepidum (Cte), Clostridium acetobutylicum (Cac), Clostridium difficile (Cdi), Enterococcus faecalis (Efa), Erwinia herbicola (Ehe), Escherichia coli (Eco), Haemophilus influenzae (Hin), Helicobacter pylori (Hpy), Klebsiella pneumoniae (Kpn), Methanobacterium thermoautotrophicum (Mth), Methanococcus jannaschii (Mjan), Mycobacterium avis (Mav), Meloidogyne javanica (Mjav), Mycobacterium bovis (Mbo), Mycobacterium tuberculosis (Mtu), Neisseria gonorrhoeae (Ngo), Neisseria meningitidis (Nme), Pasteurella multocida (Pmu), Porphyromonas gingivalis (Pgi), Pseudomonas aeruginosa (Pae), Pseudomonas fluorescens (Pfl), Pseudomonas stutzeri (Pst), Salmonella typhimurium (Sty), Shewanella putrefaciens (Spu), Sinorhizobium meliloti (Sme), Staphylococcus aureus (Sau), Streptomyces coelicolor (Sco), Streptococcus mutans (Smu), Streptococcus pneumoniae (Spn), Streptococcus pyogenes (Spy), Streptomyces coelicolor (Sco), Streptomyces pristinaespiralis (Spr), Thermotoga maritima (Tma), Thiobacillus ferrioxidans (Tfe), Vibrio cholerae (Vch), Vibrio vulnificans (Vvu), Xanthomonas campestris (Xca), and Yersinia pestis (Ype). Within the ten-member cluster of AroQPheA proteins present in enteric bacteria and their closest relatives, the S. putrefaciens (Spu) protein possesses a third domain (AroQPheAAroA). However, the AroA domain is altered at many otherwise-conserved residues and presumably lacks catalytic function (pseudogene).