>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=0 Score=1236.27 Aligned_cols=370 Identities=47% Similarity=0.784 Sum_probs=350.3 Q ss_pred EEEEECCCCEEEEEEECCCCEEEEEEEEECCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCHHHH---------CCCCC Q ss_conf 689972898799997567624888898537888876014161425617321689736845882342---------04653 Q gi|254780420|r 14 AVLVLADGSVIEGMGCGATGSIQAEICFNTSLTGYQEILTDPSYLGQIVNFTFPHIGNVGVNSEDF---------ESISR 84 (396) Q Consensus 14 A~L~LedGt~f~G~~fG~~~~~~GEvVFnT~mtGYqE~lTDPSY~gQIlvfT~P~IGNyGvn~~d~---------ES~~~ 84 (396) T Consensus 1 A~LvLeDGt~f~G~sFGa~~~~~GE~VFnTgMTGYQE~lTDPSY~GQIvv~TyP~IGNyG~n~~d~rDe~~LkYfES--- 77 (383) T TIGR01368 1 AYLVLEDGTVFEGYSFGAEGTVAGEVVFNTGMTGYQEILTDPSYKGQIVVFTYPLIGNYGVNDEDARDELGLKYFES--- 77 (383) T ss_pred CEEECCCCCEEEEEEECCCCCEEEEEEEECCCCCCCEEEECHHHCCHHHHHCCCCCCCCCCCHHHHCCCCCCEEEEE--- T ss_conf 97781378777888845666548889883689774203206200323776068752431478035200002303432--- Q ss_pred CC-CCEEEEEEEECCCCCCCCCCCCCCHHHHHHHCCCCEECCCCHHHHHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHH Q ss_conf 33-21023666404654434552417989999742783211257689999998539842366327654589789888774 Q gi|254780420|r 85 KN-FKGAVGLVIKAEITEPSNYRANMHFDAWLKSCGIIGLSGIDTRALTVWIRDYGVSNSVIAHHPDGQFDLEDLKERAK 163 (396) Q Consensus 85 ~~-~~~~~g~Iv~~~~~~~Sn~rs~~sL~~wL~~~~IpgI~GIDTRaLTk~IRe~G~~~a~I~~~~~~~~d~~~~~~~~~ 163 (396) T Consensus 78 -~~~i~v~G~vv~e~~~~~Snwra~~SL~~~L~~~~ipgI~GvDTRaLv~~iR~~G~m~g~I~~~~---~~~~~~~~~~~ 153 (383) T TIGR01368 78 -KGKIHVKGLVVRELSDRYSNWRATESLDQFLKEHGIPGIYGVDTRALVKKIREKGTMKGVISTED---SNDEELVEKAK 153 (383) T ss_pred -CCEEEEEEEEEECCCCCCCHHHHHCCHHHHHHHCCCEEEECCCHHHHHHHHHHCCCEEEEEEECC---CCHHHHHHHHH T ss_conf -88348999985412367871556504899998569847304577999999863585478996067---67035677865 Q ss_pred -HCCCCCCCCHHHCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCHHHHHHHHHCCCCEEEECCCCHHHH Q ss_conf -1588743210110133332111686534454344346777771499996796410232222202454133046574464 Q gi|254780420|r 164 -NWSGLKGAELAKHVTVSQRRDWSEKIWKWGEETSFLKSSDAKYHVVCIDYGIRSNLLRVLSSLGCRITIVGAETSYKDI 242 (396) Q Consensus 164 -~~~~~~~~dL~~~Vs~~~~~~~~~~~~~~~~~~~~~~~~~~~~kIvvIDfGiK~nIlr~L~~~g~~v~Vvp~~~~~~~i 242 (396) T Consensus 154 f~~p~~~~~nLv~~Vst~~~~~~~~~~~~~~~~~~~~~~g~~~~~Vv~~DfG~K~nIlr~L~~rG~~v~vVP~~~~~~~i 233 (383) T TIGR01368 154 FESPDIDGINLVAEVSTKEPYTWGQGTWNLWKFFVAKRNGKKPLRVVVIDFGVKQNILRRLVKRGCEVTVVPYDTDAEEI 233 (383) T ss_pred HHCCCCCCCCCCCCEECCCCEEECCCCCHHHHHHHHCCCCCCCEEEEEEECCCCHHHHHHHHHCCCEEEEECCCCCHHHH T ss_conf 42467577652010011465560688641664322113689735999985588755898997669879996789988999 Q ss_pred HHCCCCEEEECCCCCCC-CCCCCCCHHHHHHHCCCCCCEEEEECHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCEEE Q ss_conf 41357889985888884-10112110122210257863478610058878752854466776752101123477897099 Q gi|254780420|r 243 MSLQPDGVLLSNGPGDP-AVTSVYSSPIICKLVDSGMPMFGICLGHQLLGLALGAQTVKMYQGHHGVNHPVKNISNGTVE 321 (396) Q Consensus 243 ~~~~pdgi~lSnGPGdP-~~~~~~~~~~~~~~~~~~iPilGIClGhQ~l~~a~G~~~~kl~~GhrG~N~Pv~~~~t~kv~ 321 (396) T Consensus 234 ~~~~PDGiflSNGPGDPH~~~~~-~i~~~~~l~~~~~P~fGICLGHQllALA~Ga~TyKlKFGHRG~NhPV~~~~~g~v~ 312 (383) T TIGR01368 234 KKYNPDGIFLSNGPGDPHAAVEP-AIETVRELLEAKIPIFGICLGHQLLALAFGAKTYKLKFGHRGGNHPVKDLRTGRVE 312 (383) T ss_pred HHHCCCEEEEECCCCCCHHHHHH-HHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCEEECCCCCCCCCCCEEECCCCEEE T ss_conf 86578889990879880567899-99999999844897100266689999973887000465678875131442798799 Q ss_pred EECCCCCEEEEHHHCC-CCCEEEEEECCCCEEEEEEECCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 9614576157034369-982899998899808726867997789834878877670016899999999997 Q gi|254780420|r 322 IVSMNHGFAIDASSLP-AGLEETHISLFDSSNCGFRLIDQPVFSVQYHPESSPGPQDSYYLFSTFIDFMHK 391 (396) Q Consensus 322 iTsqNHg~~v~~~slp-~~~~v~~~~~nD~tiegi~~~~~~~~~vQfHPEa~PGP~D~~~~F~~F~~~i~~ 391 (396) T Consensus 313 ITsQNHGyAVD~~sl~~~~~~~th~nLNDgt~EG~~h~~~P~fSVQyHPEA~PGPhD~~~lFd~F~~~~~~ 383 (383) T TIGR01368 313 ITSQNHGYAVDEESLLAGDLEVTHVNLNDGTVEGIRHKDLPVFSVQYHPEASPGPHDTEYLFDEFIDLIKK 383 (383) T ss_pred EEEECCCEECCHHHCCCCCEEEEEEECCCCCCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHC T ss_conf 99706871257535578853899983597933153005878667700688888700237999999999819

HHsearch alignment for GI: 254780420 and conserved domain: TIGR01368