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Conserved domains on  [gi|1481289507|gb|RJF65526|]
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peptidase P60 [Rhodopseudomonas palustris]

Protein Classification

C40 family peptidase( domain architecture ID 11434971)

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

CATH:  3.90.1720.10
EC:  3.4.-.-
Gene Ontology:  GO:0008233|GO:0006508|GO:0016787|GO:0008234|GO:0000270
MEROPS:  C40
PubMed:  12620121|11517925

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
NlpC COG0791
Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];
59-280 4.04e-32

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


:

Pssm-ID: 440554 [Multi-domain]  Cd Length: 218  Bit Score: 117.88  E-value: 4.04e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507  59 GERVTVYDRTEEGWAWGQLMTDGYVGWLPDLALYRPAAEPTHKVTALRTFAFHGPSIKLPPAETLPLGARLAIVREDANF 138
Cdd:COG0791     3 VASALAAALAAAAAALAAVAAAGALAAADAAVAAALVAAAAAVLAAAALLAGPAAAVAGAAAPAVGSAGAAAAAAAAKAG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507 139 AVTQEGwylPRQHVALLADIEADFVAVAERFIGTPYLWGGRSSLGIDCSGLVQTALAACGIAAPRDSDMQeAALGAPVPL 218
Cdd:COG0791    83 SSAAKS---AAGASAPPSSTAEAIVAAALSYLGTPYVWGGTSPSGFDCSGLVQYVYRQAGISLPRTSADQ-AAAGTPVSR 158

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1481289507 219 AEqaaLKRGDLLFWK------GHVAIARDAVSIVHANAYHMATAIEPTQEAIARiaaagSALTAIKRL 280
Cdd:COG0791   159 SE---LQPGDLVFFRtggggiSHVGIYLGNGKFIHASSSGKGVRISSLDSPYWK-----SRYVGARRV 218
 
Name Accession Description Interval E-value
NlpC COG0791
Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];
59-280 4.04e-32

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


Pssm-ID: 440554 [Multi-domain]  Cd Length: 218  Bit Score: 117.88  E-value: 4.04e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507  59 GERVTVYDRTEEGWAWGQLMTDGYVGWLPDLALYRPAAEPTHKVTALRTFAFHGPSIKLPPAETLPLGARLAIVREDANF 138
Cdd:COG0791     3 VASALAAALAAAAAALAAVAAAGALAAADAAVAAALVAAAAAVLAAAALLAGPAAAVAGAAAPAVGSAGAAAAAAAAKAG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507 139 AVTQEGwylPRQHVALLADIEADFVAVAERFIGTPYLWGGRSSLGIDCSGLVQTALAACGIAAPRDSDMQeAALGAPVPL 218
Cdd:COG0791    83 SSAAKS---AAGASAPPSSTAEAIVAAALSYLGTPYVWGGTSPSGFDCSGLVQYVYRQAGISLPRTSADQ-AAAGTPVSR 158

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1481289507 219 AEqaaLKRGDLLFWK------GHVAIARDAVSIVHANAYHMATAIEPTQEAIARiaaagSALTAIKRL 280
Cdd:COG0791   159 SE---LQPGDLVFFRtggggiSHVGIYLGNGKFIHASSSGKGVRISSLDSPYWK-----SRYVGARRV 218
NLPC_P60 pfam00877
NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.
 171-252 2.59e-19

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: 80.79  E-value: 2.59e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507 171 GTPYLWGGRSSLGIDCSGLVQTALAACGIAAPRDSDMQEAALGAPVPLAEqaaLKRGDLLFWKG-----HVAIARDAVSI 245
Cdd:pfam00877   1 GVPYRWGGGSPSGFDCSGLVRYAFAKVGIELPRSSGQQYNAGKKTIPKSE---PQRGDLVFFGTgkgisHVGIYLGNGQM 77


                  ....*..
gi 1481289507 246 VHANAYH 252
Cdd:pfam00877  78 LHASTGG 84
PRK13914 PRK13914
invasion associated endopeptidase;
163-238 1.07e-07

invasion associated endopeptidase;


Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 52.50  E-value: 1.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507 163 VAVAERFIGTPYLWGGRSSLGIDCSGLVQTALAACGIAAPRDSDMQEAalgAPVPLAEQAAlKRGDLLFWK-----GHVA 237
Cdd:PRK13914  370 IAEAQKHLGKAYSWGGNGPTTFDCSGYTKYVFAKAGISLPRTSGAQYA---STTRISESQA-KPGDLVFFDygsgiSHVG 445


                  .
gi 1481289507 238 I 238
Cdd:PRK13914  446 I 446
wall_hydro_RipC NF038345
peptidoglycan hydrolase RipC; RipC is a peptidoglycan hydrolase, found in species such as ...
 170-263 1.40e-06

peptidoglycan hydrolase RipC; RipC is a peptidoglycan hydrolase, found in species such as Mycobacterium tuberculosis, that is activated by conformation change sent as a signal by the cell division-regulating transporter-like complex FtsEX. Members of this family are distinguished from more distant homologs by a Pro/Gly-rich region.


Pssm-ID: 468486 [Multi-domain]  Cd Length: 361  Bit Score: 48.96  E-value: 1.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507 170 IGTPYLWGGRSSLGIDCSGLVQTALAACGIAAPRDSDMQeAALGAPVPLAEqaaLKRGDLLFWKG---HVAIARDAVSIV 246
Cdd:NF038345  261 IGSPYSWGGSGPNAFDCSGLVMWAFQQAGISLPHSSQAL-ARGGQPVSLDD---LQPGDVVTFYSdasHAGIYIGDGMMV 336

                          90
                  ....*....|....*..
gi 1481289507 247 HANAYHMATAIEPTQEA 263
Cdd:NF038345  337 HASTYGTPVRVAPISSA 353
SH3 cd00174
Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction ...
 58-87 1.94e-03

Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction.


Pssm-ID: 212690 [Multi-domain]  Cd Length: 51  Bit Score: 35.52  E-value: 1.94e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1481289507  58 KGERVTVYDRTEEGWAWGQLMtDGYVGWLP 87
Cdd:cd00174    20 KGDIITVLEKDDDGWWEGELN-GGREGLFP 48
SH3 smart00326
Src homology 3 domains; Src homology 3 (SH3) domains bind to target proteins through sequences ...
 58-87 2.59e-03

Src homology 3 domains; Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.


Pssm-ID: 214620 [Multi-domain]  Cd Length: 56  Bit Score: 35.21  E-value: 2.59e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 1481289507   58 KGERVTVYDRTEEGWAWGQLMtDGYVGWLP 87
Cdd:smart00326  23 KGDIITVLEKSDDGWWKGRLG-RGKEGLFP 51
 
Name Accession Description Interval E-value
NlpC COG0791
Cell wall-associated hydrolase, NlpC_P60 family [Cell wall/membrane/envelope biogenesis];
59-280 4.04e-32

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


Pssm-ID: 440554 [Multi-domain]  Cd Length: 218  Bit Score: 117.88  E-value: 4.04e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507  59 GERVTVYDRTEEGWAWGQLMTDGYVGWLPDLALYRPAAEPTHKVTALRTFAFHGPSIKLPPAETLPLGARLAIVREDANF 138
Cdd:COG0791     3 VASALAAALAAAAAALAAVAAAGALAAADAAVAAALVAAAAAVLAAAALLAGPAAAVAGAAAPAVGSAGAAAAAAAAKAG 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507 139 AVTQEGwylPRQHVALLADIEADFVAVAERFIGTPYLWGGRSSLGIDCSGLVQTALAACGIAAPRDSDMQeAALGAPVPL 218
Cdd:COG0791    83 SSAAKS---AAGASAPPSSTAEAIVAAALSYLGTPYVWGGTSPSGFDCSGLVQYVYRQAGISLPRTSADQ-AAAGTPVSR 158

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1481289507 219 AEqaaLKRGDLLFWK------GHVAIARDAVSIVHANAYHMATAIEPTQEAIARiaaagSALTAIKRL 280
Cdd:COG0791   159 SE---LQPGDLVFFRtggggiSHVGIYLGNGKFIHASSSGKGVRISSLDSPYWK-----SRYVGARRV 218
NLPC_P60 pfam00877
NlpC/P60 family; The function of this domain is unknown. It is found in several lipoproteins.
 171-252 2.59e-19

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: 80.79  E-value: 2.59e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507 171 GTPYLWGGRSSLGIDCSGLVQTALAACGIAAPRDSDMQEAALGAPVPLAEqaaLKRGDLLFWKG-----HVAIARDAVSI 245
Cdd:pfam00877   1 GVPYRWGGGSPSGFDCSGLVRYAFAKVGIELPRSSGQQYNAGKKTIPKSE---PQRGDLVFFGTgkgisHVGIYLGNGQM 77


                  ....*..
gi 1481289507 246 VHANAYH 252
Cdd:pfam00877  78 LHASTGG 84
SH3_16 pfam18348
Bacterial dipeptidyl-peptidase Sh3 domain; This is the first of two N-terminal bacterial SH3 ...
 42-91 2.13e-13

Bacterial dipeptidyl-peptidase Sh3 domain; This is the first of two N-terminal bacterial SH3 (SH3b) domains found in bacterial dipeptidyl-peptidases VI such as gamma-D-glutamyl-L-diamino acid endopeptidases. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed.


Pssm-ID: 436429  Cd Length: 49  Bit Score: 63.30  E-value: 2.13e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1481289507  42 VRREPFSGAMLETEALKGERVTVYDRTEeGWAWGQLMTDGYVGWLPDLAL 91
Cdd:pfam18348   1 LRDSPDPDAELATQALFGEHLRVLEERD-GWAWVQLCEDGYVGWLPLSDL 49
PRK13914 PRK13914
invasion associated endopeptidase;
163-238 1.07e-07

invasion associated endopeptidase;


Pssm-ID: 237555 [Multi-domain]  Cd Length: 481  Bit Score: 52.50  E-value: 1.07e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507 163 VAVAERFIGTPYLWGGRSSLGIDCSGLVQTALAACGIAAPRDSDMQEAalgAPVPLAEQAAlKRGDLLFWK-----GHVA 237
Cdd:PRK13914  370 IAEAQKHLGKAYSWGGNGPTTFDCSGYTKYVFAKAGISLPRTSGAQYA---STTRISESQA-KPGDLVFFDygsgiSHVG 445


                  .
gi 1481289507 238 I 238
Cdd:PRK13914  446 I 446
wall_hydro_RipC NF038345
peptidoglycan hydrolase RipC; RipC is a peptidoglycan hydrolase, found in species such as ...
 170-263 1.40e-06

peptidoglycan hydrolase RipC; RipC is a peptidoglycan hydrolase, found in species such as Mycobacterium tuberculosis, that is activated by conformation change sent as a signal by the cell division-regulating transporter-like complex FtsEX. Members of this family are distinguished from more distant homologs by a Pro/Gly-rich region.


Pssm-ID: 468486 [Multi-domain]  Cd Length: 361  Bit Score: 48.96  E-value: 1.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507 170 IGTPYLWGGRSSLGIDCSGLVQTALAACGIAAPRDSDMQeAALGAPVPLAEqaaLKRGDLLFWKG---HVAIARDAVSIV 246
Cdd:NF038345  261 IGSPYSWGGSGPNAFDCSGLVMWAFQQAGISLPHSSQAL-ARGGQPVSLDD---LQPGDVVTFYSdasHAGIYIGDGMMV 336

                          90
                  ....*....|....*..
gi 1481289507 247 HANAYHMATAIEPTQEA 263
Cdd:NF038345  337 HASTYGTPVRVAPISSA 353
spr PRK10838
bifunctional murein DD-endopeptidase/murein LD-carboxypeptidase;
171-248 1.90e-04

bifunctional murein DD-endopeptidase/murein LD-carboxypeptidase;


Pssm-ID: 236773 [Multi-domain]  Cd Length: 190  Bit Score: 41.29  E-value: 1.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1481289507 171 GTPYLWGGRSSLGIDCSGLVQTAL-AACGIAAPRDSDMQEaALGAPVplaEQAALKRGDL-LFWKG----HVAIARDAVS 244
Cdd:PRK10838   79 GVRYRLGGSTKKGIDCSAFVQRTFrEQFGLELPRSTYEQQ-EMGKSV---SRSKLRTGDLvLFRAGstgrHVGIYIGNNQ 154


                  ....
gi 1481289507 245 IVHA 248
Cdd:PRK10838  155 FVHA 158
SH3 cd00174
Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction ...
 58-87 1.94e-03

Src Homology 3 domain superfamily; Src Homology 3 (SH3) domains are protein interaction domains that bind proline-rich ligands with moderate affinity and selectivity, preferentially to PxxP motifs. Thus, they are referred to as proline-recognition domains (PRDs). SH3 domains are less selective and show more diverse specificity compared to other PRDs. They have been shown to bind peptide sequences that lack the PxxP motif; examples include the PxxDY motif of Eps8 and the RKxxYxxY sequence in SKAP55. SH3 domain containing proteins play versatile and diverse roles in the cell, including the regulation of enzymes, changing the subcellular localization of signaling pathway components, and mediating the formation of multiprotein complex assemblies, among others. Many members of this superfamily are adaptor proteins that associate with a number of protein partners, facilitating complex formation and signal transduction.


Pssm-ID: 212690 [Multi-domain]  Cd Length: 51  Bit Score: 35.52  E-value: 1.94e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 1481289507  58 KGERVTVYDRTEEGWAWGQLMtDGYVGWLP 87
Cdd:cd00174    20 KGDIITVLEKDDDGWWEGELN-GGREGLFP 48
SH3_3 pfam08239
Bacterial SH3 domain;
38-85 2.06e-03

Bacterial SH3 domain;


Pssm-ID: 462405 [Multi-domain]  Cd Length: 54  Bit Score: 35.69  E-value: 2.06e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1481289507  38 GVAPVRREPFSGAMLETEALKGERVTVYDRTEEGWAwgQLMT-DGYVGW 85
Cdd:pfam08239   1 SGLNVRSGPSTSSEVVGTLPKGEKVEVLEEQGGGWY--KVRTyDGYEGW 47
SH3 smart00326
Src homology 3 domains; Src homology 3 (SH3) domains bind to target proteins through sequences ...
 58-87 2.59e-03

Src homology 3 domains; Src homology 3 (SH3) domains bind to target proteins through sequences containing proline and hydrophobic amino acids. Pro-containing polypeptides may bind to SH3 domains in 2 different binding orientations.


Pssm-ID: 214620 [Multi-domain]  Cd Length: 56  Bit Score: 35.21  E-value: 2.59e-03
                           10        20        30
                   ....*....|....*....|....*....|
gi 1481289507   58 KGERVTVYDRTEEGWAWGQLMtDGYVGWLP 87
Cdd:smart00326  23 KGDIITVLEKSDDGWWKGRLG-RGKEGLFP 51
 
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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