HHsearch alignment for GI: 254781096 and conserved domain: TIGR01143
>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=399.75 Aligned_cols=342 Identities=24% Similarity=0.414 Sum_probs=271.8
Q ss_pred CC--CEEEECCCCCCHHHHHHHHHHCCCCCC---EEEEECCCCCCCCCCCCC----CCCCCCHHHCCCCC-CHHHH----
Q ss_conf 85--158704578404778888640344443---057535733333100146----85420011023221-01221----
Q gi|254781096|r 107 RK--SISVSGTHGKTTTTSLIAALLEQGKFD---PTVINGGIINSYGTNARI----GTSEWIVVEADESD-GTFIR---- 172 (474)
Q Consensus 107 ~~--~IaVTGTnGKTTTt~ml~~il~~~g~~---~~~~~G~~~~~~~~~~~~----~~~~~~V~E~~e~~-~s~~~---- 172 (474)
T Consensus 82 ~~~~~igiTGS~GKTTtKEm~~~iL~~~~~~~~aV~~t~GN~Nn~iGlPltlL~~~~~~~~aV~EmG~s~~GEI~~L~~i 161 (462)
T TIGR01143 82 AKRRVIGITGSSGKTTTKEMLAAILSHKYKDSEAVLATPGNFNNEIGLPLTLLRATEDHDYAVLEMGASHPGEIAYLAEI 161 (462)
T ss_pred CCEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEECCCCCCCCHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHHH
T ss_conf 97589998568960679999999998535975323624887676135678875078888059998438988737899986
Q ss_pred CCCCCEEEEEEECCCHHH---CCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHCC--CCC-CCCCCCCC-CCC
Q ss_conf 185530342220220110---00255666643013333332222222346501345432001--112-33333332-222
Q gi|254781096|r 173 LPSDIVVVTNIDPEHLDY---YGDFNAIRAAFYKFIDNIPFYGFAVVCMDHPEVRSLIARIQ--NRK-IITYGRHP-QAD 245 (474)
Q Consensus 173 ~~P~iaVitNI~~DHld~---~~s~e~y~~aK~~i~~~~~~~g~~vin~Dd~~~~~~~~~~~--~~~-v~~fg~~~-~~d 245 (474)
T Consensus 162 ~~P~ia~itNi~~AHl~~F~~Fgs~~~Ia~aK~EI~~~~~~~~~a~~n~d~~~~~~~~~~~~~~~~~~~~~Fg~~~~~~d 241 (462)
T TIGR01143 162 AKPDIALITNIGEAHLEGFGDFGSLEGIAEAKGEILQGLKENGIAVINADDPALAKFKKRLKILNKAKVLSFGLEGKYAD 241 (462)
T ss_pred HCCCEEEEECCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCHHHHHHHHHCCCCCCCCEEEECCCCCCCC
T ss_conf 19986999170478761157875389999999999707897758985352568899998411157864788147776343
Q ss_pred EEEEEEEECCCCCEEEEEEECCCCCCCCCCCCCCCC-CCCCC-CCCCCCCCCCHHHHHHCHHHHHHHHHHCCCCCCCCEE
Q ss_conf 022102112584201355511344444200002356-76543-3322112100123210000001334310000158221
Q gi|254781096|r 246 IRYSNIRKYSGRSIFDVSVQGNVTKDLTVIKDLSLP-LIGEH-NISNACASIAVAYKLGLSSEDVKKGLASFSGIKRRFT 323 (474)
Q Consensus 246 ~~~~~i~~~~~~~~f~~~~~~~~~~~~~~~~~~~l~-l~G~H-n~~NalaAia~a~~lgi~~e~i~~~L~~f~g~~~R~e 323 (474)
T Consensus 242 ~~~~~~~~~~~g~~f~~~~~~~~~-------~v~LP~~~G~h~n~~NalaA~Ala~~lG~~~~~~~~gL~~~~~~~gR~~ 314 (462)
T TIGR01143 242 VSAEDVSLSELGTGFTLVTPGGEI-------EVELPILLGRHPNVENALAAAALALALGLPLEEIAEGLSELKPVKGRLE 314 (462)
T ss_pred EEEECCEECCCCCEEEEEECCCEE-------EEEECCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCEE
T ss_conf 688432121533358998637089-------9983112088188999999999999809888899989764278876507
Q ss_pred EECCCCCEEEEEE-CCCCCCCCHHHHHHHHCCC-----CCCCEEEEECCCCHHH-HHHHHHHHHHHH--HCCEEEEECCC
Q ss_conf 1014786047630-2445543022233310134-----4321033303663147-888999999986--18999990866
Q gi|254781096|r 324 LVGVWNDVHVFDD-YGHHPIEISSVLAAVRQIC-----PRKIIAIHQPHRYSRL-STLFDQFSSCFG--DADIVLISPVY 394 (474)
Q Consensus 324 ~v~~~~gv~~idD-yahnP~~i~atl~al~~~~-----~~rii~i~~p~~~sr~-~~~~~e~~~~l~--~ad~vil~~i~ 394 (474)
T Consensus 315 ~~~~~~g~~~IdD~YNAnp~Sm~AAl~~L~~~~~~~E~g~~~~VLG~M~ELG~~s~~~H~~vg~~a~~~~~~~~~~~--- 391 (462)
T TIGR01143 315 VIQTKKGLTLIDDTYNANPDSMRAALDALARFPGKGEVGKKILVLGDMLELGELSEELHAEVGRYAAALGIDLVFLV--- 391 (462)
T ss_pred EEEECCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEE---
T ss_conf 89864874898441359889999999996138888863546899838453117999999999999986287389984---
Q ss_pred CCCCCCCCCCCHHHHHHHHHHCC---CCCEEEECCHHHHHHHHH----HHCCCCCEEEEECCCCHHHHHHHHHHHH
Q ss_conf 67764323899999999999638---998999889899999999----8558987999944899889999999998
Q gi|254781096|r 395 SAGEKEIPGFSSPELVKNIKLQG---HPQAYYMDSFDHLVSKIL----AIAEPGDFIIFFGAGNITQWAASLIGEL 463 (474)
Q Consensus 395 ~~~e~~~~g~~~~~l~~~i~~~~---~~~~~~~~~~~eav~~~~----~~~~~gDvVL~~GaG~~~~~~~~~~~~l 463 (474)
T Consensus 392 --G~~~~~-~~~~~~~~~~~~~e~~~~~~~~~f~~~~~l~~~L~~~~~~~~~~~~~vLvKGSR~~~l--e~vv~~L 462 (462)
T TIGR01143 392 --GEEASP-NTVAVIADSLGSGEKLVKKQGKHFADKDELLAFLKDLNELQVGEGDVVLVKGSRSVKL--EKVVEAL 462 (462)
T ss_pred --CCCCCC-HHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHHCCCCCCCEEEEECCCHHHH--HHHHHCC
T ss_conf --773350-2699999985589650468887517988999998753311257860899953642367--8998409