>TIGR01143 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; InterPro: IPR005863 The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages: (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer. Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC) and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales . This entry represents UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF, 6.3.2.15 from EC), which is required to catalyze the final step in the synthesis of the cytoplasmic precursor of the bacterial cell wall peptidoglycan. ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine.. The crystal structure of the MurF apo-enzyme has been determined and refined to 2.3 A resolution. It contains three consecutive open alpha/beta-sheet domains. The topology of the N-terminal domain of MurF is unique, while its central and C-terminal domains exhibit similar mononucleotide and dinucleotide-binding folds to MurD. The apo-enzyme of MurF crystal structure reveals an open conformation with the three domains juxtaposed in a crescent-like arrangement creating a wide-open space where substrates are expected to bind. As such, catalysis is not feasible and significant domain closure is expected upon substrate binding . ; GO: 0005524 ATP binding, 0008766 UDP-N-acetylmuramoylalanyl-D-glutamyl-26-diaminopimelate-D-alanyl-D-alanine ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.

Probab=100.00 E-value=0 Score=387.54 Aligned_cols=331 Identities=21% Similarity=0.274 Sum_probs=262.0 Q ss_pred CCCCCC--EEEEECCCCCCHHHHHHHHHHHHHHH----HCCCCCC----CCCCCCCCCCCCCCCEEEEECC-CCC--C-C Q ss_conf 156886--89960345752157899999987310----0000001----2443221101688837999217-754--3-2 Q gi|254781099|r 109 SSLQSP--FIAVTGTNGKSSTVALISHVLRKNGY----DVQLGGN----IGLPILNLEYFSPNRFYVIECS-SYQ--I-E 174 (468) Q Consensus 109 ~~~~~~--vI~VTGT~GKTTt~~ll~~iL~~~g~----~~~~~GN----iG~p~~~~~~~~~~~~~V~E~S-SfQ--L-~ 174 (468) T Consensus 78 ~~~~~~~~~igiTGS~GKTTtKEm~~~iL~~~~~~~~aV~~t~GN~Nn~iGlPltlL~~~~~~~~aV~EmG~s~~GEI~~ 157 (462) T TIGR01143 78 EKFSAKRRVIGITGSSGKTTTKEMLAAILSHKYKDSEAVLATPGNFNNEIGLPLTLLRATEDHDYAVLEMGASHPGEIAY 157 (462) T ss_pred HHCCCCEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEECCCCCCCCHHHHHHHHCCCCCCCEEEEEECCCCCCCHHH T ss_conf 74399758999856896067999999999853597532362488767613567887507888805999843898873789 Q ss_pred CCCCCCCCCCEEEEECCCHHHH---HHHHHHCCCCCCCEEEE---CCCCCCCCCCHHHHHHHHHCCCCCCE-EECCCCCC Q ss_conf 1223332210111002101222---11100001122100010---13443224786789998740123430-11036443 Q gi|254781099|r 175 LTPTIDPSIGVLLNISPDHLDR---HHTLENYVNIKKKIVTM---SKHAIICINDHQCEKIAYDMNFIGHS-ISRISSQS 247 (468) Q Consensus 175 ~~~~~~PdiavITNI~~DHLd~---~~s~e~y~~aK~~i~~~---~~~~iln~dd~~~~~~~~~~~~~~~~-~~~~~~~~ 247 (468) T Consensus 158 L~~i~~P~ia~itNi~~AHl~~F~~Fgs~~~Ia~aK~EI~~~~~~~~~a~~n~d~~~~~~~~~~~~~~~~~~~~~Fg~~~ 237 (462) T TIGR01143 158 LAEIAKPDIALITNIGEAHLEGFGDFGSLEGIAEAKGEILQGLKENGIAVINADDPALAKFKKRLKILNKAKVLSFGLEG 237 (462) T ss_pred HHHHHCCCEEEEECCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCHHHHHHHHHCCCCCCCCEEEECCCC T ss_conf 99861998699917047876115787538999999999970789775898535256889999841115786478814777 Q ss_pred -----CCCCCCEEECCCEEEECCCCCCCCCCCC-CCCCH-HHHHCCCHHHHHHCCCCCCCCCHHHCCCHHHHHHHHHHHC Q ss_conf -----2223411212413541467642123455-88510-1110011012221022222110000000013454433210 Q gi|254781099|r 248 -----LQSDSDLYIDESFLKCSATSEVIFDFSQ-ETKKH-NIQNLVTSAVVCMQLGLKVEEIKRALLSCGGLTHRLQTIA 320 (468) Q Consensus 248 -----~~~~~~~~~~~~~~~~~~~~~~~~~~~~-l~G~H-Ni~NalaAia~a~~lGi~~~~i~~~L~~f~gv~~R~E~i~ 320 (468) T Consensus 238 ~~~d~~~~~~~~~~~g~~f~~~~~~~~~~v~LP~~~G~h~n~~NalaA~Ala~~lG~~~~~~~~gL~~~~~~~gR~~~~~ 317 (462) T TIGR01143 238 KYADVSAEDVSLSELGTGFTLVTPGGEIEVELPILLGRHPNVENALAAAALALALGLPLEEIAEGLSELKPVKGRLEVIQ 317 (462) T ss_pred CCCCEEEECCEECCCCCEEEEEECCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCEEEEE T ss_conf 63436884321215333589986370899983112088188999999999999809888899989764278876507898 Q ss_pred CCCCCEEECCCCCCCHHHHHHHHHC---CC-----CCCEEEECCCCCCCCH-----HHHHHHHC--CCCEEEEECCCH-- Q ss_conf 0343000002355675555553201---33-----3200120321012206-----89899842--786899988998-- Q gi|254781099|r 321 RLGHVIFINDSKATNLHSVIHAFLN---EK-----RRIYWIAGGLSKSDDF-----STLFPFIS--KIAKAYFIGNSA-- 383 (468) Q Consensus 321 ~~~gv~iIDDS~atnp~a~~~Al~~---~~-----~~i~lI~GG~~K~~d~-----~~L~~~~~--~~~~~~liG~~~-- 383 (468) T Consensus 318 ~~~g~~~IdD~YNAnp~Sm~AAl~~L~~~~~~~E~g~~~~VLG~M~ELG~~s~~~H~~vg~~a~~~~~~~~~~~G~~~~~ 397 (462) T TIGR01143 318 TKKGLTLIDDTYNANPDSMRAALDALARFPGKGEVGKKILVLGDMLELGELSEELHAEVGRYAAALGIDLVFLVGEEASP 397 (462) T ss_pred ECCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC T ss_conf 64874898441359889999999996138888863546899838453117999999999999986287389984773350 Q ss_pred ---HHHHHHHHC-----CCCEEEECCHHHHHHHHHHH-HHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHC Q ss_conf ---998886316-----89889987999999999999-984489859994522166313479899999999999863 Q gi|254781099|r 384 ---MLFFHHFGG-----KINSTLSKTLDQALKSVVRD-VENVQLPSIVLFSPGCASFDQYNNFRERGFSFMSQVSEI 451 (468) Q Consensus 384 ---~~i~~~~~~-----~~~~~~~~~~~~a~~~i~~~-~~~~~~gDiVLlSPa~aS~d~f~~y~~RG~~F~~~v~~l 451 (468) T Consensus 398 ~~~~~~~~~~~~~e~~~~~~~~~f~~~~~l~~~L~~~~~~~~~~~~~vLvK---GS---------R~~~le~vv~~L 462 (462) T TIGR01143 398 NTVAVIADSLGSGEKLVKKQGKHFADKDELLAFLKDLNELQVGEGDVVLVK---GS---------RSVKLEKVVEAL 462 (462) T ss_pred HHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHHCCCCCCCEEEEE---CC---------CHHHHHHHHHCC T ss_conf 269999998558965046888751798899999875331125786089995---36---------423678998409

HHsearch alignment for GI: 254781099 and conserved domain: TIGR01143