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Conserved domains on  [gi|2472162543|dbj|BDI46034|]
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phage tail assembly protein [Escherichia sp. HH154_1D]

Protein Classification

C40 family peptidase( domain architecture ID 11674318)

C40 family peptidase is a cell-wall hydrolase that cleaves peptide cross-bridges between glycan chains and is essential for bacterial growth and viability; typically cleaves the linkage between D-Glu and diaminopimelic acid (or Lys) within peptidoglycan stem peptides; contains a Cys-His-His catalytic triad; also contains a Mpr1p, Pad1p N-terminal (MPN) domain that may have catalytic isopeptidase activity

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
MPN super family cl13996
Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) ...
1-60 1.57e-25

Mpr1p, Pad1p N-terminal (MPN) domains; MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+) domains are found in the N-terminal termini of proteins with a variety of functions; they are components of the proteasome regulatory subunits, the signalosome (CSN), eukaryotic translation initiation factor 3 (eIF3) complexes, and regulators of transcription factors. These domains are isopeptidases that release ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. Catalytically active MPN domains contain a metalloprotease signature known as the JAB1/MPN/Mov34 metalloenzyme (JAMM) motif. For example, Rpn11 (also known as POH1 or PSMD14), a subunit of the 19S proteasome lid is involved in the ATP-dependent degradation of ubiquitinated proteins, contains the conserved JAMM motif involved in zinc ion coordination. Poh1 is a regulator of c-Jun, an important regulator of cell proliferation, differentiation, survival and death. JAB1 is a component of the COP9 signalosome (CSN), a regulatory particle of the ubiquitin (Ub)/26S proteasome system occurring in all eukaryotic cells; it cleaves the ubiquitin-like protein NEDD8 from the cullin subunit of the SCF (Skp1, Cullins, F-box proteins) family of E3 ubiquitin ligases. AMSH (associated molecule with the SH3 domain of STAM, also known as STAMBP), a member of JAMM/MPN+ deubiquitinases (DUBs), specifically cleaves Lys 63-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. Similarly, BRCC36, part of the nuclear complex that includes BRCA1 protein and is targeted to DNA damage foci after irradiation, specifically disassembles K63-linked polyUb. BRCC36 is aberrantly expressed in sporadic breast tumors, indicative of a potential role in the pathogenesis of the disease. Some variants of the JAB1/MPN domains lack key residues in their JAMM motif and are unable to coordinate a metal ion. Comparisons of key catalytic and metal binding residues explain why the MPN-containing proteins Mov34/PSMD7, Rpn8, CSN6, Prp8p, and the translation initiation factor 3 subunits f (p47) and h (p40) do not show catalytic isopeptidase activity. It has been proposed that the MPN domain in these proteins has a primarily structural function.


The actual alignment was detected with superfamily member cd08073:

Pssm-ID: 472685  Cd Length: 108  Bit Score: 95.06  E-value: 1.57e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2472162543   1 MSPEDWLRAEMQGEIVALVHSHPGGLPWLSEADRRLQVQSDLPWWLVCR--GAIHKFRCVPH 60
Cdd:cd08073    47 ISPEDYAAAEDEGEIVAVVHSHPDGSPAPSEADRAQQEATGLPWIIVSWpeGDLRVFRPVGY 108
NLPC_P60 super family cl21534
NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.
63-176 1.22e-13

NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.


The actual alignment was detected with superfamily member pfam00877:

Pssm-ID: 473902 [Multi-domain]  Cd Length: 105  Bit Score: 64.23  E-value: 1.22e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2472162543  63 GRRFEHG-----VTDCYTLFRDAYHLAGIEMPDFHRgdDWWRNGQNlyldnleatglyQVPLSAAQPGDVLLccFGS-SV 136
Cdd:pfam00877   1 GVPYRWGggspsGFDCSGLVRYAFAKVGIELPRSSG--QQYNAGKK------------TIPKSEPQRGDLVF--FGTgKG 64
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2472162543 137 PNHAAIYCGDGELLHHIP-EQLSKRERYTDKWQRRTHSLWR 176
Cdd:pfam00877  65 ISHVGIYLGNGQMLHASTgGGVSISSLNGGYWQKRLVGVRR 105
 
Name Accession Description Interval E-value
MPN_NLPC_P60 cd08073
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) ...
1-60 1.57e-25

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains; This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.


Pssm-ID: 163704  Cd Length: 108  Bit Score: 95.06  E-value: 1.57e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2472162543   1 MSPEDWLRAEMQGEIVALVHSHPGGLPWLSEADRRLQVQSDLPWWLVCR--GAIHKFRCVPH 60
Cdd:cd08073    47 ISPEDYAAAEDEGEIVAVVHSHPDGSPAPSEADRAQQEATGLPWIIVSWpeGDLRVFRPVGY 108
NLPC_P60 pfam00877
NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.
63-176 1.22e-13

NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.


Pssm-ID: 395705 [Multi-domain]  Cd Length: 105  Bit Score: 64.23  E-value: 1.22e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2472162543  63 GRRFEHG-----VTDCYTLFRDAYHLAGIEMPDFHRgdDWWRNGQNlyldnleatglyQVPLSAAQPGDVLLccFGS-SV 136
Cdd:pfam00877   1 GVPYRWGggspsGFDCSGLVRYAFAKVGIELPRSSG--QQYNAGKK------------TIPKSEPQRGDLVF--FGTgKG 64
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2472162543 137 PNHAAIYCGDGELLHHIP-EQLSKRERYTDKWQRRTHSLWR 176
Cdd:pfam00877  65 ISHVGIYLGNGQMLHASTgGGVSISSLNGGYWQKRLVGVRR 105
Rri1 COG1310
Proteasome lid subunit RPN8/RPN11, contains Jab1/MPN domain metalloenzyme (JAMM) motif ...
1-48 2.76e-10

Proteasome lid subunit RPN8/RPN11, contains Jab1/MPN domain metalloenzyme (JAMM) motif [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440921  Cd Length: 127  Bit Score: 55.69  E-value: 2.76e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2472162543   1 MSPEDWLRA-----EMQGEIVALVHSHPGGLPWLSEADRRLQVQSDLPWWLVC 48
Cdd:COG1310    57 IDPEDLLAAerearERGLEIVGIYHSHPDGPAYPSETDRAQAAWPGLPYLIVS 109
NlpC COG0791
Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];
72-151 1.56e-08

Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440554 [Multi-domain]  Cd Length: 218  Bit Score: 52.78  E-value: 1.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2472162543  72 DCYTLFRDAYHLAGIEMPdfHRGDDWWRNGQnlyldnleatglyQVPLSAAQPGDVLLccFGSS--VPNHAAIYCGDGEL 149
Cdd:COG0791   126 DCSGLVQYVYRQAGISLP--RTSADQAAAGT-------------PVSRSELQPGDLVF--FRTGggGISHVGIYLGNGKF 188

                  ..
gi 2472162543 150 LH 151
Cdd:COG0791   189 IH 190
JAB_MPN smart00232
JAB/MPN domain; Domain in Jun kinase activation domain binding protein and proteasomal ...
1-44 1.53e-04

JAB/MPN domain; Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.


Pssm-ID: 214573  Cd Length: 135  Bit Score: 40.05  E-value: 1.53e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2472162543    1 MSPEDWLRAEMQGEIVALVHSHPGGLPWLSEADRRLQVQSDLPW 44
Cdd:smart00232  64 LMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPW 107
 
Name Accession Description Interval E-value
MPN_NLPC_P60 cd08073
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) ...
1-60 1.57e-25

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding) found in proteins also containing NlpC/P60 domains; This family contains bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains at the N-terminus of NlpC/P60 phage tail protein domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.


Pssm-ID: 163704  Cd Length: 108  Bit Score: 95.06  E-value: 1.57e-25
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2472162543   1 MSPEDWLRAEMQGEIVALVHSHPGGLPWLSEADRRLQVQSDLPWWLVCR--GAIHKFRCVPH 60
Cdd:cd08073    47 ISPEDYAAAEDEGEIVAVVHSHPDGSPAPSEADRAQQEATGLPWIIVSWpeGDLRVFRPVGY 108
MPN_prok_mb cd08059
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
5-58 2.24e-21

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); prokaryotic; This family contains bacterial and archaeal MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These catalytically active domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.


Pssm-ID: 163690  Cd Length: 101  Bit Score: 84.15  E-value: 2.24e-21
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2472162543   5 DWLRAEMQGEIVALVHSHPGGLPWLSEADRRLQVQSDLPWWLVCRGAIHKFRCV 58
Cdd:cd08059    48 DLAALEIGMKVVGLVHSHPSGSCRPSEADLSLFTRFGLYHVIVCYPYENSWKCY 101
NLPC_P60 pfam00877
NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.
63-176 1.22e-13

NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.


Pssm-ID: 395705 [Multi-domain]  Cd Length: 105  Bit Score: 64.23  E-value: 1.22e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2472162543  63 GRRFEHG-----VTDCYTLFRDAYHLAGIEMPDFHRgdDWWRNGQNlyldnleatglyQVPLSAAQPGDVLLccFGS-SV 136
Cdd:pfam00877   1 GVPYRWGggspsGFDCSGLVRYAFAKVGIELPRSSG--QQYNAGKK------------TIPKSEPQRGDLVF--FGTgKG 64
                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 2472162543 137 PNHAAIYCGDGELLHHIP-EQLSKRERYTDKWQRRTHSLWR 176
Cdd:pfam00877  65 ISHVGIYLGNGQMLHASTgGGVSISSLNGGYWQKRLVGVRR 105
Rri1 COG1310
Proteasome lid subunit RPN8/RPN11, contains Jab1/MPN domain metalloenzyme (JAMM) motif ...
1-48 2.76e-10

Proteasome lid subunit RPN8/RPN11, contains Jab1/MPN domain metalloenzyme (JAMM) motif [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440921  Cd Length: 127  Bit Score: 55.69  E-value: 2.76e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2472162543   1 MSPEDWLRA-----EMQGEIVALVHSHPGGLPWLSEADRRLQVQSDLPWWLVC 48
Cdd:COG1310    57 IDPEDLLAAerearERGLEIVGIYHSHPDGPAYPSETDRAQAAWPGLPYLIVS 109
NlpC COG0791
Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];
72-151 1.56e-08

Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 440554 [Multi-domain]  Cd Length: 218  Bit Score: 52.78  E-value: 1.56e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2472162543  72 DCYTLFRDAYHLAGIEMPdfHRGDDWWRNGQnlyldnleatglyQVPLSAAQPGDVLLccFGSS--VPNHAAIYCGDGEL 149
Cdd:COG0791   126 DCSGLVQYVYRQAGISLP--RTSADQAAAGT-------------PVSRSELQPGDLVF--FRTGggGISHVGIYLGNGKF 188

                  ..
gi 2472162543 150 LH 151
Cdd:COG0791   189 IH 190
MPN_like cd08070
Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); ...
1-57 1.85e-05

Mpr1p, Pad1p N-terminal (MPN) domains with catalytic isopeptidase activity (metal-binding); This family contains archaeal and bacterial MPN (also known as Mov34, PAD-1, JAMM, JAB, MPN+)-like domains. These domains contain the signature JAB1/MPN/Mov34 metalloenzyme (JAMM) motif, EXnHS/THX7SXXD, which is involved in zinc ion coordination and provides the active site for isopeptidase activity for the release of ubiquitin from ubiquitinated proteins (thus having deubiquitinating (DUB) activity) that are tagged for degradation. The JAMM proteins likely hydrolyze ubiquitin conjugates in a manner similar to thermolysin, in which the zinc-polarized aqua ligand serves as the nucleophile, compared with the classical DUBs that do so with a cysteine residue in the active site.


Pssm-ID: 163701  Cd Length: 128  Bit Score: 42.63  E-value: 1.85e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2472162543   1 MSPEDWLRAEMQG-----EIVALVHSHPGGLPWLSEADRRLQVQSDLPWWLVC-RGAIHKFRC 57
Cdd:cd08070    53 IDPAEQLAAQREArerglEVVGIYHSHPDGPARPSETDLRLAWPPGVSYLIVSlAGGAPELRA 115
JAB_MPN smart00232
JAB/MPN domain; Domain in Jun kinase activation domain binding protein and proteasomal ...
1-44 1.53e-04

JAB/MPN domain; Domain in Jun kinase activation domain binding protein and proteasomal subunits. Domain at Mpr1p and Pad1p N-termini. Domain of unknown function.


Pssm-ID: 214573  Cd Length: 135  Bit Score: 40.05  E-value: 1.53e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
gi 2472162543    1 MSPEDWLRAEMQGEIVALVHSHPGGLPWLSEADRRLQVQSDLPW 44
Cdd:smart00232  64 LMDEELKKVNKDLEIVGWYHSHPDESPFPSEVDVATHESYQAPW 107
 
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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