>TIGR00763 lon ATP-dependent protease La; InterPro: IPR004815 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This signature defines the bacterial and eukaryotic lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). This family of sequences does not include the archaeal lon homologs, IPR004663 from INTERPRO. In the eukaryotes the majority of the proteins are located in the mitochondrial matrix , . In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response .; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0006510 ATP-dependent proteolysis.

Probab=99.63 E-value=3.3e-15 Score=127.02 Aligned_cols=245 Identities=24% Similarity=0.340 Sum_probs=171.1 Q ss_pred HHHHHHHHHHCCCHHHHHHHHH--HHHH--HHHHHHHCCC--CCCCCC-CCCCCEEEEECCCCCHHHHHHHHHHHHCCCE Q ss_conf 8999997420308599999999--9998--6588752121--013552-2568358840733217699999998718531 Q gi|254780271|r 69 QEILRVLDEYVIGQGQAKKVLA--VAVH--NHYKRLAHSS--KSSNVE-LAKSNILLVGPTGCGKTYLAQTLARIIDVPF 141 (424) Q Consensus 69 ~eI~~~Ld~yVIGQ~~AKkavA--vAv~--nh~rR~~~~~--~~~~~e-i~~~NILliGPTGvGKTelAr~LAk~l~~PF 141 (424) T Consensus 403 ~~A~~~LD~DHYGL~~VK~RIlEYlAV~qllemrrkkkPkL~~~~~GpqI----lClvGPPGVGKTSlg~SIA~ALnRkF 478 (941) T TIGR00763 403 KRAKEILDEDHYGLKKVKERILEYLAVQQLLEMRRKKKPKLRGKMKGPQI----LCLVGPPGVGKTSLGKSIAKALNRKF 478 (941) T ss_pred HHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEE----EEEECCCCCCHHHHHHHHHHHHCCEE T ss_conf 99999831678888773034135888989998764036444778888767----87207269542227899999968804 Q ss_pred EEHHHHHH---HHH-----HHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC--CCCCCCCCCCCCCHHHHHHH Q ss_conf 31012211---111-----103556330357788765422776542233322333200--23333334432102568988 Q gi|254780271|r 142 TMADATTL---TEA-----GYVGEDVENIILKLLQAADYNVERAQRGIVYIDEVDKIS--RKSDNPSITRDVSGEGVQQA 211 (424) Q Consensus 142 ~~vdaT~~---TE~-----GYvG~Dvesii~~L~~~a~~~v~~a~~~iv~iDEidKi~--~~~~~~~~~~dvs~~gvq~~ 211 (424) T Consensus 479 vR~SlGG~~DeAEIrGHRRTYvGAMPGriiQ~lk~~~t~------NPl~LlDEIDK~~~~~~-----~~GDPaS-----A 542 (941) T TIGR00763 479 VRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTK------NPLILLDEIDKIGLKSS-----FRGDPAS-----A 542 (941) T ss_pred EEEEECCCEEHHHCCCCCCCCCCCCHHHHHHHHHHCCCC------CCEEEEEEEEEECCCCC-----CCCCHHH-----H T ss_conf 999526722031127864320346725789998760415------88068620220016788-----6556378-----8 Q ss_pred HHHHCCCCEEECCCCCCCCCCCCCEEEEECCHHH--HHHHCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHH Q ss_conf 7531058701025655643222430243100012--32200046789887641234333211110000000168999641 Q gi|254780271|r 212 LLKIMEGTIASVPPQGGRKHPQQEFLQVDTTNIL--FICGGAFAGLDRIISARGEKASIGFSAVVKDSDNRPVGEVLRNL 289 (424) Q Consensus 212 LLkileg~~~~v~~~~grk~~~~~~~~Idt~nil--fi~~gaf~~l~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 (424) T Consensus 543 LLEvLDPEQN~------~F~DHYldvp~DLS~V~CyFi~TAN~~--d~I------------------------------- 583 (941) T TIGR00763 543 LLEVLDPEQNN------AFSDHYLDVPFDLSKVLCYFIATANSI--DTI------------------------------- 583 (941) T ss_pred HHHHCCHHHCC------CCCCCCCCCCCCHHHHHHHEEECCCCC--CCC------------------------------- T ss_conf 86412864360------425530023400420021000244757--677------------------------------- Q ss_pred HHHHHHHHCHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECHHHHHHHHHHHHHCCCCCH Q ss_conf 05677752206898720784267211105789999874267799999999874498999968999999995510678742 Q gi|254780271|r 290 ESEDLVKFGLIPEFIGRLPVLATLEDLDENSLIRILSEPKNALIKQYQCLFDMEDVELVFHEDALREIARCAIAHKTGAR 369 (424) Q Consensus 290 ~~~DL~~~gliPEl~GRlPiiV~L~~Lt~edl~rILtepknsLikQy~~Ll~~egV~L~FtdeAi~~IA~~A~~~niGAR 369 (424) T Consensus 584 ------P----~PLLDRM-EvI~lsGY~~~EK~~IA---~~yLiP~~~~~~GL~~~~l~~~d~al~~lI~-~YtREaGVR 648 (941) T TIGR00763 584 ------P----RPLLDRM-EVIELSGYTEEEKLEIA---KKYLIPKALEDHGLKPDELKISDEALLLLIK-YYTREAGVR 648 (941) T ss_pred ------C----CCCCCCE-EEEECCCCCHHHHHHHH---HHCCHHHHHHHHCCCCCCEEECHHHHHHHHH-HHHHHHCCH T ss_conf ------7----2213740-24523888767899999---8547136798708881322126899999998-751320213 Q ss_pred HHHHHHHHHHHHHHHCCC Q ss_conf 368999999677740276 Q gi|254780271|r 370 GLRSILEKILLDTMFELP 387 (424) Q Consensus 370 ~LrtIiE~iLedimFe~P 387 (424) T Consensus 649 NL~r~I~~i~RK~A~~~~ 666 (941) T TIGR00763 649 NLERQIEKICRKAAVKLV 666 (941) T ss_pred HHHHHHHHHHHHHHHHHH T ss_conf 389999999999999998

HHsearch alignment for GI: 254780271 and conserved domain: TIGR00763