double-psi beta-barrel fold of YuiC subfamily proteins; The YuiC subfamily includes a group of conserved double-psi beta-barrel (DPBB) fold proteins, such as Bacillus subtilis protein YuiC, cell wall shaping protein YabE, cell wall-binding protein YocH, as well as Clostridium tetani phosphatase-associated protein PapQ. YuiC is a Firmicute stationary phase survival (Sps) protein that closely resembles the Barwin-like endoglucanase beta barrel of MltA. It is a double-psi beta-barrel (DPBB) fold that consists of two interlocked "psi-structure" motifs related by a pseudo-2-fold axis and may be involved in substrate binding and catalysis.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359827680 248 KVLDMSATAYTASYKDTkkhpdHPLFGITYTGVRVKR-GIVAVDPKVIPLGTRLYIEGlgdtpdYGYAVAADIGSAIKGN 326
Cdd:cd22786    2 KKITVEATAYSPCSSSG-----GGCYGITASGTPLKRkGTIAVDPSVIPLGTKVYIPG------YGYAVVADTGGAIKGN 70

                         90       100
                 ....*....|....*....|....*
gi 359827680 327 KIDLYVETQSEADRFGRRKVRVYVL 351
Cdd:cd22786   71 RIDLYFPTHEEAINWGRKTVEVYVL 95

cell wall-binding protein EntB; This HMM describes the cell wall-binding protein EntB, as found in Bacillus cereus. EntB is related to EntA, EntC, and EndD. All Ent family proteins have a signal peptide, an N-terminal SH3 domain and a C-terminal 3D (Asp-Asp-Asp) domain. EntB and EndC have a central region with a highly variable number of repeats resembling KAXEXX. The gene symbol derives from the notion that at least some members of the family function as enterotoxins, but more recent descriptions focus on roles in stress response and cell wall integrity.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359827680 238 VSRGEVIRYKKVLDMSATAYTASYKDTKKHPDHPL--FGITYTGVRVKRgIVAVDPKVIPLGTRLYIEGlgdtpdYGYAV 315
Cdd:NF040676 368 ASKNNIQSAKRELTVVATAYTADPSENGTYGGRVLtaMGHDLTANPNMR-IIAVDPKVIPLGSKVWVEG------YGEAI 440

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 359827680 316 AADIGSAIKGNKIDLYVETQSEADRFGRRKVRVYVL 351
Cdd:NF040676 441 AGDTGSAIKGNRIDVLMGSKSKAMNWGRQTVKVKIL 476

3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases [Function unknown]; 3D (Asp-Asp-Asp) domain, usually in lytic transglycosylases is part of the Pathway/BioSystem: 3D

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359827680 251 DMSATAYTASYKDTKKHPdhplfGITYTGVRVKR-GIVAVDPKVIPLGTRLYIEGlgdtpdYGYAVAADIGSAIKGNKID 329
Cdd:COG3584    1 TVTATAYTAGPECTGKGG-----GITASGTRLRPgGVIAVDPDVIPLGTKVYIEG------YGYAVAEDTGGAIKGNRID 69

                         90       100
                 ....*....|....*....|..
gi 359827680 330 LYVETQSEADRFGRRKVRVYVL 351
Cdd:COG3584   70 IYMPSVSEALNWGRRTVTVYIL 91

Non-mltA associated 3D domain containing proteins, named for 3 conserved aspartate residues; This family contains the 3D domain, named for its 3 conserved aspartates, including similar uncharacterized proteins. These proteins contain the critical active site aspartate of mltA-like lytic transglycosylases where the 3D domain forms a larger domain with the N-terminal region. This domain is also found in conjunction with numerous other domains such as the Escherichia coli MltA, a membrane-bound lytic transglycosylase comprised of 2 domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, corresponding to the 3D domain and Domain B is inserted within the linear sequence of domain A. MltA is distinct from other bacterial LTs, which are similar to each other. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. PG chains (also known as murein), the major components of the bacterial cell wall, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), and lytic transglycosylases cleave this beta-1-4 bond.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359827680 252 MSATAYTASYKDTKKHPdhplFGITYTGVRVKRGIVAVDPKVIPLGTRLYIEGlgdtpdYGYAVAADIGSAIKGNKIDLY 331
Cdd:cd14667    1 FTATAYTSCEGCCGGGP----GGTASGGLPVGGGTIAVDPSVIPLGTKVYIEG------YGVYVVEDTGGAIKGNRIDIY 70

                         90       100
                 ....*....|....*....|
gi 359827680 332 VETQSEADRFGRRKVRVYVL 351
Cdd:cd14667   71 MDSHAEALAFGRRYVEVYIL 90

3D domain, named for 3 conserved aspartate residues, is found in mltA-like lytic transglycosylases and numerous other contexts; This family contains the 3D domain, named for its 3 conserved aspartates. It is found in conjunction with numerous other domains such as MltA (membrane-bound lytic murein transglycosylase A). These aspartates are critical active site residues of mltA-like lytic transglycosylases. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. MltA has 2 domains, separated by a large groove, where the peptidoglycan strand binds. The C-terminus has a double-psi beta barrel fold within the 3D domain, which forms the larger A domain along with the N-terminal region of Mlts, but is also found in various other domain architectures. Peptigoglycan (also known as murein) chains, the primary structural component of bacterial cells walls, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc); lytic transglycosylases (LTs) cleave this beta-1-4 bond. Typically, LTs are exolytic, releasing Metabolite 1 (GlcNAc-anhMurNAc-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala) from the ends of the PG strands. In contrast, membrane-bound lytic murein transglycosylase E (MltE) is endolytic , cleaving in the middle of PG strands, with further processing to Metabolite 1 accomplished by other LTs. In E. coli, there are six membrane- bound LTs: MltA-MltF and soluble Slt70. Slt35 is a soluble fragment cleaved from MltB. Bacterial LTs are classified in 4 families: Family 1 includes slt70 MltC-MltF, Family 2 includes MltA, Family 3 includes MltB, and family 4 of bacteriophage origin. While most LTs are related members of the lysozyme-like lytic transglycosylase family, MltA represents a distinct fold and sequence conservation.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 359827680 253 SATAYTASY-KDTKKHPDHP--LFGITYTGVRVK-RGIVAVDPKVIPLGTRLYIEGLGDTPDYGYAVAADIGSAIKGNKI 328
Cdd:cd14486    2 QATGYTEWDdGKRPSPPDEFsfSFRLTASGRPPVpYRTIAVDPSVIPLGSVVYIPELRGLPNDGVFVAEDTGGAIKGNHI 81

                         90       100
                 ....*....|....*....|...
gi 359827680 329 DLYVETQSEADRFGRRKVRVYVL 351
Cdd:cd14486   82 DVYTGDGPDARSNALKTVTVYVV 104

G5 domain; This domain is found in a wide range of extracellular proteins. It is found tandemly repeated in up to 8 copies. It is found in the N-terminus of peptidases belonging to the M26 family which cleave human IgA. The domain is also found in proteins involved in metabolism of bacterial cell walls suggesting this domain may have an adhesive function.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 359827680  160 ELVTKNEIIPYEIDRRPNNSMDQGVEQVVNKGKDGVCEKTYKVVYEDGKEVERKLISDTIVKEPEKEIVEYGT 232
Cdd:pfam07501   2 KTVTEEEEIPFETVTKEDPSLPKGEEKVVQEGKPGEKEVTYKVTYVNGKEVSREVVSEEVTKEPVDEVVAVGT 74

double-psi beta-barrel fold of membrane-bound lytic murein transglycosylase A (MltA) and similar proteins; MltA, also called murein hydrolase A, is a murein-degrading enzyme that may play a role in the recycling of muropeptides during cell elongation and/or cell division. It degrades murein glycan strands and insoluble, high-molecular weight murein sacculi. Bacterial lytic transglycosylases (LTs) are classified into 4 families: family 1 includes slt70 MltC-MltF, family 2 includes MltA, family 3 includes MltB, and family 4 includes proteins of bacteriophage origin. MltA is distinct from other bacterial LTs, which are similar in structure and sequence with a lysozyme-like fold. MltA is a kidney bean-shaped monomeric protein comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which corresponds to a double-psi beta-barrel (DPBB) fold. Domain B also has a beta-barrel fold topology, but it is inserted within the linear sequence of domain A. This model corresponds to the DPBB fold that consists of two interlocked "psi-structure" motifs related by a pseudo-2-fold axis. It is involved in substrate binding and catalysis.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 359827680 287 VAVDPKVIPLGTRLYIEGL------GDTPDYGYAVAADIGSAIKGNKIDLYVETQSEADRFG---RRKVRVYVL 351
Cdd:cd22785   24 VAVDPSVIPLGSVVYIPALdgvklpDGEPHDGLFIAQDTGGAIKGKHIDVFTGSGDEAGELAgklNHTGRVYVL 97

Domain A of MltA and related lytic transglycosylase; domain A is interrupted by domain B; Escherichia coli MltA is a membrane-bound lytic transglycosylase comprised of two domains separated by a large groove, where the peptidoglycan strand binds. Domain A is made up of an N-terminal and a C-terminal portion, which correspond to the 3D domain, named for 3 conserved aspartate residues. Domain B is inserted within the linear sequence of domain A. MltA is distinct from other bacterial lytic transglycosylases (LTs), which are similar to each other. Escherichia coli peptidoglycan lytic transglycosylase (LT) initiates cell wall recycling in response to damage, during bacterial fission, and cleaves peptidoglycan (PG) to create functional spaces in its wall. PG chains (also known as murein), the major components of the bacterial cell wall, are comprised of alternating beta-1-4-linked N-acetylmuramic acid (MurNAc) and N-acetyl-D-glucosamine (GlcNAc), and lytic transglycosylases cleave this beta-1-4 bond. Typically, peptidoglycan lytic transglycosylases (LT) are exolytic, releasing Metabolite 1 (GlcNAc-anhMurNAc-L-Ala-D-Glu-m-Dap-D-Ala-D-Ala) from the ends of the PG strands. In contrast, MltE is endolytic , cleaving in the middle of PG strands, with further processing to Metabolite 1 accomplished by other LTs. In E. coli, there are six membrane-bound LTs: MltA-MltF and soluble Slt70. Slt35 is a soluble fragment cleaved from MltB. Bacterial LTs are classified in 4 families: Family 1 includes slt70 MltC-MltF, Family 2 includes MltA, Family 3 includes MltB, and Family 4 of bacteriophage origin. While most of the LT family members are similar in structure and sequence with a lysozyme-like fold, Family 2 (including mltA) is distinct.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 359827680 287 VAVDPKVIPLGTRLYIEglGDTPDYGYA--------VAADIGSAIKG-NKIDLYV----ETQSEADRFgRRKVRVYVL 351
Cdd:cd14485   85 LAVDRSLIPLGAPVWLE--TPLPDANGGgkplrrlvIAQDTGGAIKGpVRADLFWgsgdEAGELAGRM-KHPGRLWVL 159

G5-linked-Ubiquitin-like domain; This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593. This protein is involved in sporulation part of the SET3C complex, which is required to repress early/middle sporulation genes during meiosis. The bacterial proteins are likely to be involved in a cell wall function as they are found in conjunction with the pfam07501 domain, which is involved in various cell surface processes. This domain is also present in the resuscitation-promoting factors RpfB from Mycobacterium tuberculosis and Rpf2 from Corynebacterium glutamicum. These are factors that stimulate resuscitation of dormant cells. This domain has a beta grasp fold. Structural description of this domain revealed a structural conservation between these domains and ubiquitin, hence it is termed UBL-G5.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 359827680  102 IKVFADGKETTVMTSKDTVEEALKNSSIGLGDLDRIE 138
Cdd:pfam03990   1 VTLTVDGKERTVTTTAGTVGDLLEEAGITLGEHDKVS 37