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Conserved domains on  [gi|112803662|gb|EAU01006|]
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UDP-2,3-diacylglucosamine hydrolase [Campylobacter curvus 525.92]

Protein Classification

UDP-2,3-diacylglucosamine diphosphatase( domain architecture ID 10164688)

UDP-2,3-diacylglucosamine diphosphatase catalyzes the fourth step of lipid A biosynthesis, in which a precursor UDP-2,3-diacylglucosamine is hydrolyzed to yield 2,3-diacylglucosamine 1-phosphate and UMP; belongs to the metallophosphoesterase (MPP) superfamily

CATH:  3.60.21.10
EC:  3.6.1.54
Gene Ontology:  GO:0008758|GO:0046872|GO:0009245
PubMed:  25837850
SCOP:  3001067

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
MPP_YbbF-LpxH cd07398
Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an ...
 19-227 4.42e-49

Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an Escherichia coli UDP-2,3-diacylglucosamine hydrolase thought to catalyze the fourth step of lipid A biosynthesis, in which a precursor UDP-2,3-diacylglucosamine is hydrolyzed to yield 2,3-diacylglucosamine 1-phosphate and UMP. YbbF belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


:

Pssm-ID: 277343 [Multi-domain]  Cd Length: 217  Bit Score: 160.99  E-value: 4.42e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  19 VFIADAHENLGAGRDGFLeFLRAVDEGCIIASQLFLMGDMFDFLCGYADNTVKIYAEHIA-LINKIAQKIQVFYIEGNHD 97
Cdd:cd07398    1 LFISDLHLGLRGCRADRL-LDFLLVEELDEADALYLLGDIFDLWIGDDSVVWPGAHRALArLLRLADRGTEVIYVPGNHD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  98 FGLAPIFKNVEIFPIQKQPANFKTQDENSVAIAHGDIFLPPITKYALLFLRLRWFL-------KIMNFIDRICKFKISNA 170
Cdd:cd07398   80 FLLGRFFAEALGAILLPEPAEHLELDGKRLLVLHGDQLDTDDRAYQWLRKLGRNPYlqllflnLPLNRRRRIAGLIRRSS 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 112803662 171 I-LTKLKFKKLDYEISNFSGFIAPKMRHYEARIVIEGHYHQGKIFNINNKFYINLPAF 227
Cdd:cd07398  160 AaYLKHKQKKALAIIDVFEEAVARLARHRGVDGVICGHTHRPAIHRLDGILYINLGDW 217
 
Name Accession Description Interval E-value
MPP_YbbF-LpxH cd07398
Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an ...
 19-227 4.42e-49

Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an Escherichia coli UDP-2,3-diacylglucosamine hydrolase thought to catalyze the fourth step of lipid A biosynthesis, in which a precursor UDP-2,3-diacylglucosamine is hydrolyzed to yield 2,3-diacylglucosamine 1-phosphate and UMP. YbbF belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277343 [Multi-domain]  Cd Length: 217  Bit Score: 160.99  E-value: 4.42e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  19 VFIADAHENLGAGRDGFLeFLRAVDEGCIIASQLFLMGDMFDFLCGYADNTVKIYAEHIA-LINKIAQKIQVFYIEGNHD 97
Cdd:cd07398    1 LFISDLHLGLRGCRADRL-LDFLLVEELDEADALYLLGDIFDLWIGDDSVVWPGAHRALArLLRLADRGTEVIYVPGNHD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  98 FGLAPIFKNVEIFPIQKQPANFKTQDENSVAIAHGDIFLPPITKYALLFLRLRWFL-------KIMNFIDRICKFKISNA 170
Cdd:cd07398   80 FLLGRFFAEALGAILLPEPAEHLELDGKRLLVLHGDQLDTDDRAYQWLRKLGRNPYlqllflnLPLNRRRRIAGLIRRSS 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 112803662 171 I-LTKLKFKKLDYEISNFSGFIAPKMRHYEARIVIEGHYHQGKIFNINNKFYINLPAF 227
Cdd:cd07398  160 AaYLKHKQKKALAIIDVFEEAVARLARHRGVDGVICGHTHRPAIHRLDGILYINLGDW 217
LpxH COG2908
UDP-2,3-diacylglucosamine pyrophosphatase LpxH [Cell wall/membrane/envelope biogenesis];
18-237 1.63e-23

UDP-2,3-diacylglucosamine pyrophosphatase LpxH [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442152 [Multi-domain]  Cd Length: 238  Bit Score: 94.87  E-value: 1.63e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  18 AVFIADAHenLGAGR-----DGFLEFLRavdEGCIIASQLFLMGDMFDFLCGYADNTVKIYAEHIALINKIAQK-IQVFY 91
Cdd:COG2908    3 TLFISDLH--LGTPGpqaitAALLDFLR---SIAHDADALYLLGDIFDFWIGDDDVWPPGHNRVLQKLLELADKgTPVYY 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  92 IEGNHDFGLAPIFK---NVEIFPiqkQPAnFKTQDENSVAIAHGDIFLPPITKYallflrlRWFLKImnFIDRICKF--- 165
Cdd:COG2908   78 IPGNHDFLLGDYFAkelGATLLP---DPI-HLTLDGKRFLLLHGDGLDTGDKGY-------QLLRKL--VRNPWLQWlfl 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662 166 --------KISNAILTKLKFKKLDYE---ISNFSGFIAPKMRHYEARIVIEGHYHQGKIFNINNKF-YINLPAFACDRSF 233
Cdd:COG2908  145 glplwsrlALAAKLRRKSKAANQDKAvkiIDVFEQAVAELARERGVDGVIHGHTHRPAIHELDGGVrYINLGDWVESGTA 224


                 ....
gi 112803662 234 FVVE 237
Cdd:COG2908  225 LVED 228
PRK05340 PRK05340
UDP-2,3-diacylglucosamine hydrolase; Provisional
 19-98 2.19e-07

UDP-2,3-diacylglucosamine hydrolase; Provisional


Pssm-ID: 235420  Cd Length: 241  Bit Score: 50.19  E-value: 2.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  19 VFIADAHenLGAGR----DGFLEFLR--AVDegciiASQLFLMGDMFDFLCGyaDNTVKIYAEHIA-LINKIAQK-IQVF 90
Cdd:PRK05340   4 LFISDLH--LSPERpaitAAFLRFLRgeARQ-----ADALYILGDLFEAWIG--DDDPSPFAREIAaALKALSDSgVPCY 74


                 ....*...
gi 112803662  91 YIEGNHDF 98
Cdd:PRK05340  75 FMHGNRDF 82
 
Name Accession Description Interval E-value
MPP_YbbF-LpxH cd07398
Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an ...
 19-227 4.42e-49

Escherichia coli YbbF/LpxH and related proteins, metallophosphatase domain; YbbF/LpxH is an Escherichia coli UDP-2,3-diacylglucosamine hydrolase thought to catalyze the fourth step of lipid A biosynthesis, in which a precursor UDP-2,3-diacylglucosamine is hydrolyzed to yield 2,3-diacylglucosamine 1-phosphate and UMP. YbbF belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277343 [Multi-domain]  Cd Length: 217  Bit Score: 160.99  E-value: 4.42e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  19 VFIADAHENLGAGRDGFLeFLRAVDEGCIIASQLFLMGDMFDFLCGYADNTVKIYAEHIA-LINKIAQKIQVFYIEGNHD 97
Cdd:cd07398    1 LFISDLHLGLRGCRADRL-LDFLLVEELDEADALYLLGDIFDLWIGDDSVVWPGAHRALArLLRLADRGTEVIYVPGNHD 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  98 FGLAPIFKNVEIFPIQKQPANFKTQDENSVAIAHGDIFLPPITKYALLFLRLRWFL-------KIMNFIDRICKFKISNA 170
Cdd:cd07398   80 FLLGRFFAEALGAILLPEPAEHLELDGKRLLVLHGDQLDTDDRAYQWLRKLGRNPYlqllflnLPLNRRRRIAGLIRRSS 159

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 112803662 171 I-LTKLKFKKLDYEISNFSGFIAPKMRHYEARIVIEGHYHQGKIFNINNKFYINLPAF 227
Cdd:cd07398  160 AaYLKHKQKKALAIIDVFEEAVARLARHRGVDGVICGHTHRPAIHRLDGILYINLGDW 217
LpxH COG2908
UDP-2,3-diacylglucosamine pyrophosphatase LpxH [Cell wall/membrane/envelope biogenesis];
18-237 1.63e-23

UDP-2,3-diacylglucosamine pyrophosphatase LpxH [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442152 [Multi-domain]  Cd Length: 238  Bit Score: 94.87  E-value: 1.63e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  18 AVFIADAHenLGAGR-----DGFLEFLRavdEGCIIASQLFLMGDMFDFLCGYADNTVKIYAEHIALINKIAQK-IQVFY 91
Cdd:COG2908    3 TLFISDLH--LGTPGpqaitAALLDFLR---SIAHDADALYLLGDIFDFWIGDDDVWPPGHNRVLQKLLELADKgTPVYY 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  92 IEGNHDFGLAPIFK---NVEIFPiqkQPAnFKTQDENSVAIAHGDIFLPPITKYallflrlRWFLKImnFIDRICKF--- 165
Cdd:COG2908   78 IPGNHDFLLGDYFAkelGATLLP---DPI-HLTLDGKRFLLLHGDGLDTGDKGY-------QLLRKL--VRNPWLQWlfl 144

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662 166 --------KISNAILTKLKFKKLDYE---ISNFSGFIAPKMRHYEARIVIEGHYHQGKIFNINNKF-YINLPAFACDRSF 233
Cdd:COG2908  145 glplwsrlALAAKLRRKSKAANQDKAvkiIDVFEQAVAELARERGVDGVIHGHTHRPAIHELDGGVrYINLGDWVESGTA 224


                 ....
gi 112803662 234 FVVE 237
Cdd:COG2908  225 LVED 228
PRK05340 PRK05340
UDP-2,3-diacylglucosamine hydrolase; Provisional
 19-98 2.19e-07

UDP-2,3-diacylglucosamine hydrolase; Provisional


Pssm-ID: 235420  Cd Length: 241  Bit Score: 50.19  E-value: 2.19e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  19 VFIADAHenLGAGR----DGFLEFLR--AVDegciiASQLFLMGDMFDFLCGyaDNTVKIYAEHIA-LINKIAQK-IQVF 90
Cdd:PRK05340   4 LFISDLH--LSPERpaitAAFLRFLRgeARQ-----ADALYILGDLFEAWIG--DDDPSPFAREIAaALKALSDSgVPCY 74


                 ....*...
gi 112803662  91 YIEGNHDF 98
Cdd:PRK05340  75 FMHGNRDF 82
MPP_Cdc1_like cd07384
Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain; Cdc1 (also ...
 51-102 7.46e-03

Saccharomyces cerevisiae CDC1 and related proteins, metallophosphatase domain; Cdc1 (also known as XlCdc1 in Xenopus laevis) is an endoplasmic reticulum-localized transmembrane lipid phosphatase with a metallophosphatase domain facing the ER lumen. In budding yeast, the gene encoding CDC1 is essential while nonlethal mutations cause defects in Golgi inheritance and actin polarization. Cdc1 mutant cells accumulate an unidentified phospholipid, suggesting that Cdc1 is a lipid phosphatase. Cdc1 mutant cells also have highly elevated intracellular calcium levels suggesting a possible role for Cdc1 in calcium regulation. The 5' flanking region of Cdc1 is a regulatory region with conserved binding site motifs for AP1, AP2, Sp1, NF-1 and CREB. DNA polymerase delta consists of at least four subunits - Pol3, Cdc1, Cdc27, and Cdm1. This group also contains Saccharomyces cerevisiae TED1 (Trafficking of Emp24p/Erv25p-dependent cargo disrupted 1), which acts together with Emp24p and Erv25p in cargo exit from the ER, and human MPPE1. The human MPPE1 gene is a candidate susceptibility gene for bipolar disorder. These proteins belong to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal active site made up of residues located at the C-terminal side of the sheets. This domain is thought to allow for productive metal coordination.


Pssm-ID: 277330 [Multi-domain]  Cd Length: 172  Bit Score: 36.17  E-value: 7.46e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 112803662  51 QLFLMGDMFDflcGYADNTVKIYAEHIALINKIAQK--------IQVFYIEGNHDFGLAP 102
Cdd:cd07384   48 VVLFLGDLFD---GGRILDSEEWKEYLHRFQKIFFLkspgslgsIPVIFIPGNHDIGYGG 104
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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