HHsearch alignment for GI: 254780827 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=96.86  E-value=0.0021  Score=42.90  Aligned_cols=59  Identities=27%  Similarity=0.300  Sum_probs=41.2

Q ss_pred             HHHH-HHHHHHHHHHHCCCCCCCCCE--EEEEECCCCCCHHHHHHHHHHHHHHCCC-CCEEEEEECCC
Q ss_conf             9999-998999998716776678767--9995278666733799999999973389-86899950887
Q gi|254780827|r   60 VNSA-KITCHQYNKFLNLKEESKIPF--VVGITGSVAVGKSTFARILCILLQQISN-FKVSLITTDGF  123 (311)
Q Consensus        60 ~~~~-~~~~~~~~~fl~~~~~~k~Pf--IIGIAG~~asGKST~Ar~L~~lL~~~~~-~~V~lis~DgF  123 (311)
T Consensus        61 V~DtV~~AL~~lA~~~~~~---~~~~~~~igiTGS--~GKTTtKEm~~~iL~~~~~~~~aV~~t~GN~  123 (462)
T TIGR01143        61 VDDTVLAALQALASAKREK---FSAKRRVIGITGS--SGKTTTKEMLAAILSHKYKDSEAVLATPGNF  123 (462)
T ss_pred             EECHHHHHHHHHHHHHHHH---CCCCEEEEEEECC--CCHHHHHHHHHHHHHHHCCCCCCEEECCCCC
T ss_conf             8065899999999999974---3997589998568--9606799999999985359753236248876