>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=1.6e-43 Score=288.02 Aligned_cols=349 Identities=21% Similarity=0.218 Sum_probs=228.4 Q ss_pred CCC-HHHHHHHHHHCCCHHHHCC-C--EEEEECCCCHHHHHHHHHHHHHHCCCC-EEEEECCCCCEEEEEEEECCCCCCC Q ss_conf 788-8999999987299588359-8--399945898479999999999997893-5141378411012008988847787 Q gi|254780821|r 3 ADS-LLKMGYLLEDLGRPQDRLP-P--VIHIGGTNGKGSVASFSQRLLETSGLS-VHVHTSPHLIRWNERFRLGVKGGRG 77 (429) Q Consensus 3 ~~~-l~r~~~ll~~lg~P~~~~~-~--vI~VtGTnGKttt~~~i~~il~~~g~k-~g~~tSPhl~~~~Eri~i~~~~~~g 77 (429) T Consensus 62 ~DtV~~AL~~lA~~~~~---~~~~~~~~igiTGS~GKTTtKEm~~~iL~~~~~~~~aV~~t~-----------------G 121 (462) T TIGR01143 62 DDTVLAALQALASAKRE---KFSAKRRVIGITGSSGKTTTKEMLAAILSHKYKDSEAVLATP-----------------G 121 (462) T ss_pred ECHHHHHHHHHHHHHHH---HCCCCEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEECC-----------------C T ss_conf 06589999999999997---439975899985689606799999999985359753236248-----------------8 Q ss_pred EECCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHH--HHHHHHCCCCCCCEEEEEECCCHHC Q ss_conf 15588999999999863047767795789999999874114462477764447--5676413567751589860250000 Q gi|254780821|r 78 RLVEDVELLDVFRRVRRVKSAQNLTIFELSIATALVLFSKYPADCAIIEVGLG--GSLDATNIIEKVAVSVITSISLDHE 155 (429) Q Consensus 78 ~~i~~~~~~~~~~~i~~~~~~~~~t~FE~lt~~a~~~f~~~~~d~~vlE~GlG--Gr~DaTnvi~~~~vavITnI~~DHl 155 (429) T Consensus 122 N~Nn~i--------------GlPltl----------L~~~~~~~~aV~EmG~s~~GEI~~L~~i~~P~ia~itNi~~AHl 177 (462) T TIGR01143 122 NFNNEI--------------GLPLTL----------LRATEDHDYAVLEMGASHPGEIAYLAEIAKPDIALITNIGEAHL 177 (462) T ss_pred CCCCCH--------------HHHHHH----------HCCCCCCCEEEEEECCCCCCCHHHHHHHHCCCEEEEECCHHHHH T ss_conf 767613--------------567887----------50788880599984389887378999861998699917047876 Q ss_pred CC---CCCCHHHHHHHHHHHCC---CCCCCCCCCCCCHHHHHHHHHHHHHCCCC-CCCCCCCC-----CC-----CCCCC Q ss_conf 00---27852344566653113---79833154447178988999986210566-52357632-----10-----12585 Q gi|254780821|r 156 KI---LGNTVSAIAKDKSGIIK---PGCPVVIGHQVYDEVREILVSKAEKMGCP-YNVYGDDF-----YA-----FEKNK 218 (429) Q Consensus 156 e~---LG~tle~Ia~eKa~I~k---~~~~~v~~~~~~~~~~~~i~~~a~~~~~~-~~~~~~~~-----~~-----~~~~~ 218 (429) T Consensus 178 ~~F~~Fg-s~~~Ia~aK~EI~~~~~~~~~a~~n~d~-~-~~~~~~~~~~~~~~~~~~~Fg~~~~~~d~~~~~~~~~~~g~ 254 (462) T TIGR01143 178 EGFGDFG-SLEGIAEAKGEILQGLKENGIAVINADD-P-ALAKFKKRLKILNKAKVLSFGLEGKYADVSAEDVSLSELGT 254 (462) T ss_pred HCCCCCC-HHHHHHHHHHHHHHCCCCCCEEEECCCC-H-HHHHHHHHCCCCCCCCEEEECCCCCCCCEEEECCEECCCCC T ss_conf 1157875-3899999999997078977589853525-6-88999984111578647881477763436884321215333 Q ss_pred EEEEEECCCCCCCCCCC-CCCCC-CCCCHHHHHHHHHHHHHCCHHHHCCCCCCCCC-CCCCEEEEECCCCCCCCCCCCEE Q ss_conf 24443103333444444-32222-11111469999875320000110011222233-66530354228754445787459 Q gi|254780821|r 219 CLVYQDKISQTNLTVLG-LVGEH-QYINAATAICAVQMAGFTLEKECINAALQSVQ-WFGRLQKITEGPLLNKLPDHSEV 295 (429) Q Consensus 219 ~~~~~~~~~~~~~~~l~-l~G~h-n~~Na~~Aiaa~~~lg~~i~~~~I~~gL~~~~-~pGR~e~i~~~~~~~~~~~~~~v 295 (429) T Consensus 255 ~f~~~~~~~~~-~v~LP~~~G~h~n~~NalaA~Ala~~lG~~~--~~~~~gL~~~~~~~gR~~~~~~~-------~g~-~ 323 (462) T TIGR01143 255 GFTLVTPGGEI-EVELPILLGRHPNVENALAAAALALALGLPL--EEIAEGLSELKPVKGRLEVIQTK-------KGL-T 323 (462) T ss_pred EEEEEECCCEE-EEEECCCCCCHHHHHHHHHHHHHHHHHCCCH--HHHHHHHHHCCCCCCCEEEEEEC-------CCE-E T ss_conf 58998637089-9983112088188999999999999809888--89998976427887650789864-------874-8 Q ss_pred EEECCC--CHHHHHHHHHHHHHHCCCC-CCCEEEEECCCCC--C----CHHHHHHHHHHHC-CEEEEEEECCCCCCCCCC Q ss_conf 993363--2157998886543311477-7712431134679--8----9899999888638-889998422889984212 Q gi|254780821|r 296 WIDGGH--NPNAGLVVSKEISKLKGSS-NKPFYLVIGMVEG--K----KYGRYLEAFVELS-PIVLSVSLICRGRERQSI 365 (429) Q Consensus 296 iiD~AH--Np~s~~~l~~~l~~l~~~~-~~~i~~I~G~~~d--K----d~~~~l~~l~~~~-d~i~~~~~~~~~~~~~~~ 365 (429) T Consensus 324 ~IdD~YNAnp~Sm~AAl~~L~~~~~~~E~g~~~~VLG~M~ELG~~s~~~H~~vg~~a~~~~~~~~~~~G~------~~~~ 397 (462) T TIGR01143 324 LIDDTYNANPDSMRAALDALARFPGKGEVGKKILVLGDMLELGELSEELHAEVGRYAAALGIDLVFLVGE------EASP 397 (462) T ss_pred EEECCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEECC------CCCC T ss_conf 9844135988999999999613888886354689983845311799999999999998628738998477------3350 Q ss_pred CCCHHHHHHHHHHC----CCCEEEECCHHHHHHHHHHH--CCCCCCCEEEEECCHHH Q ss_conf 78989999999854----99789969989999999986--03588679999497799 Q gi|254780821|r 366 SITPKVLMQEAKKL----GFQAMACSSMIEALSRVRKI--NEELPPPLILIAGSLYL 416 (429) Q Consensus 366 ~~~~~~l~~~~~~~----~~~~~~~~~~~eAi~~a~~~--~~~~~~d~VLV~GS~yl 416 (429) T Consensus 398 -~~~~~~~~~~~~~e~~~~~~~~~f~~~~~l~~~L~~~~~~~~~~~~~vLvKGSR~~ 453 (462) T TIGR01143 398 -NTVAVIADSLGSGEKLVKKQGKHFADKDELLAFLKDLNELQVGEGDVVLVKGSRSV 453 (462) T ss_pred -HHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHHCCCCCCCEEEEECCCHH T ss_conf -26999999855896504688875179889999987533112578608999536423

HHsearch alignment for GI: 254780821 and conserved domain: TIGR01143