>TIGR01368 CPSaseIIsmall carbamoyl-phosphate synthase, small subunit; InterPro: IPR006274 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains . This entry represents the small subunit of the glutamine-dependent form (6.3.5.5 from EC) of carbamoyl phosphate synthase, CPSase II. The small subunit catalyses the hydrolysis of glutamine to ammonia, which in turn used by the large chain to synthesize carbamoyl phosphate. The C-terminal domain of the small subunit of CPSase has glutamine amidotransferase activity. Note that the sequence from the mammalian urea cycle form has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I (6.3.4.16 from EC). CPSases of pyrimidine biosynthesis, arginine biosynthesis, and the urea cycle may be encoded by one or by several genes, depending on the species. ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.

Probab=100.00  E-value=2.7e-33  Score=258.13  Aligned_cols=172  Identities=27%  Similarity=0.486  Sum_probs=134.8

Q ss_pred             CEEEEEECCCCHHHHHHHHHHHCCCEEEEECCCCCHHHHHHCCCCEEEECCCCCCCCCC-CCC----CCCHHHHHCCCCE
Q ss_conf             86999988970578899888865940698528989889972399799998538899999-997----5376898089988
Q gi|254780414|r    8 SKVLIIDFGSQFTQLIARRVRESKVYCEVIAFKNALDYFKEQNPQAIILSGSPASSLDI-DSP----QIPKEILESNIPL   82 (520)
Q Consensus         8 ~~IlIlDfGSQytqLIaRriRelgVyseI~P~~~~~e~i~~~~p~GIILSGGP~SV~d~-~ap----~~~~~I~~~~iPI   82 (520)
T Consensus       197 ~~Vv~~DfG~K~n--Ilr~L~~rG~~v~vVP~~~~~~~i~~~~PDGiflSNGPG---DPH~~~~~~i~~~~~l~~~~~P~  271 (383)
T TIGR01368       197 LRVVVIDFGVKQN--ILRRLVKRGCEVTVVPYDTDAEEIKKYNPDGIFLSNGPG---DPHAAVEPAIETVRELLEAKIPI  271 (383)
T ss_pred             EEEEEEECCCCHH--HHHHHHHCCCEEEEECCCCCHHHHHHHCCCEEEEECCCC---CCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             5999985588755--898997669879996789988999865788899908798---80567899999999998448971


Q ss_pred             EEECHHHHHHHHHCCCEEEECCCCCCCEEEEEECCCCCCCCCCCCCCCCEEEEEE---CCCHHH--CCC-CCCCEEECCC
Q ss_conf             9977899998997096999869866103667523886222787266553368600---220110--124-4421123239
Q gi|254780414|r   83 LGICYGQQIMCQSLGGKTKNSQSREFGRAFIEIKKNCSLLKGMWEKGSKQQVWMS---HGDQVE--HIP-EGFEVIASSD  156 (520)
Q Consensus        83 LGICyG~QlLa~~~GG~V~~~~~~EyG~~~I~i~~~~~lf~gl~~~~~~~~VwmS---H~D~V~--~lP-~gf~viA~S~  156 (520)
T Consensus       272 fGICLGHQllALA~Ga~TyKlKFGHRG~-------NhPV~~-~----~~g~v~ITsQNHGyAVD~~sl~~~~~~~th~nL  339 (383)
T TIGR01368       272 FGICLGHQLLALAFGAKTYKLKFGHRGG-------NHPVKD-L----RTGRVEITSQNHGYAVDEESLLAGDLEVTHVNL  339 (383)
T ss_pred             CCCCHHHHHHHHHCCCCEEECCCCCCCC-------CCCEEE-C----CCCEEEEEEECCCEECCHHHCCCCCEEEEEEEC
T ss_conf             0026668999997388700046567887-------513144-2----798799997068712575355788538999835


Q ss_pred             -CCCEEEEEECCCCEEEEEEEEHHHCCCHHHH-HHHHHHHHH
Q ss_conf             -8317889863500112465212221520257-799875501
Q gi|254780414|r  157 -STPFAFIADEKRKYYAVQFHPEVVHTVGGSQ-LIDNFVHHV  196 (520)
Q Consensus       157 -~~~iaai~~~~~~iyGVQFHPEV~hT~~G~~-iL~NFl~~I  196 (520)
T Consensus       340 NDgt~EG~~h~~~P~fSVQyHPEA~PGPhD~~~lFd~F~~~~  381 (383)
T TIGR01368       340 NDGTVEGIRHKDLPVFSVQYHPEASPGPHDTEYLFDEFIDLI  381 (383)
T ss_pred             CCCCCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             979331530058786677006888887002379999999998