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Conserved domains on  [gi|489242342|ref|WP_003150552|]
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MULTISPECIES: mercury resistance system periplasmic binding protein MerP [Pseudomonadota]

Protein Classification

heavy-metal-associated domain-containing protein( domain architecture ID 317)

heavy-metal-associated domain-containing protein such as bacterial mercuric transport protein periplasmic component that acts as a mercury scavenger by specifically binding to a mercuric ion in the periplasm and probably passing it to the cytoplasmic mercuric reductase MerA via the mercuric transport protein MerT

CATH:  3.30.70.100
Gene Ontology:  GO:0046872
PubMed:  12443926|8905098
SCOP:  4001253

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HMA super family cl00207
Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid ...
 1-91 8.40e-24

Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.


The actual alignment was detected with superfamily member TIGR02052:

Pssm-ID: 469658 [Multi-domain]  Cd Length: 92  Bit Score: 86.24  E-value: 8.40e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489242342   1 MRKLLIAV-LFALPFVALAAPPKTVTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEA 79
Cdd:TIGR02052  1 MKKLATLLaLFVLTSLPAWAATQTVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEA 80

                         90
                 ....*....|..
gi 489242342  80 TANAGYPSTVQK 91
Cdd:TIGR02052 81 TTDAGYPSSLKQ 92
 
Name Accession Description Interval E-value
MerP TIGR02052
mercuric transport protein periplasmic component; This model represents the periplasmic ...
 1-91 8.40e-24

mercuric transport protein periplasmic component; This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403). [Cellular processes, Detoxification]


Pssm-ID: 131107 [Multi-domain]  Cd Length: 92  Bit Score: 86.24  E-value: 8.40e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489242342   1 MRKLLIAV-LFALPFVALAAPPKTVTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEA 79
Cdd:TIGR02052  1 MKKLATLLaLFVLTSLPAWAATQTVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEA 80

                         90
                 ....*....|..
gi 489242342  80 TANAGYPSTVQK 91
Cdd:TIGR02052 81 TTDAGYPSSLKQ 92
CopZ COG2608
Copper chaperone CopZ [Inorganic ion transport and metabolism];
22-91 2.30e-23

Copper chaperone CopZ [Inorganic ion transport and metabolism];


Pssm-ID: 442020 [Multi-domain]  Cd Length: 71  Bit Score: 84.57  E-value: 2.30e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489242342 22 KTVTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEATANAGYPSTVQK 91
Cdd:COG2608   2 KTVTLKVEGMTCGHCVARVEKALKALDGVASVEVDLATGTATVTYDPEKVSLEDIKAAIEEAGYEVEKAE 71
HMA cd00371
Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid ...
 25-88 9.27e-19

Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.


Pssm-ID: 238219 [Multi-domain]  Cd Length: 63  Bit Score: 72.64  E-value: 9.27e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489242342 25 TLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDkAQPEALTEATANAGYPST 88
Cdd:cd00371   1 ELSVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPE-VSPEELLEAIEDAGYKAR 63
HMA pfam00403
Heavy-metal-associated domain;
25-79 4.66e-14

Heavy-metal-associated domain;


Pssm-ID: 459804 [Multi-domain]  Cd Length: 58  Bit Score: 60.33  E-value: 4.66e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489242342  25 TLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEA 79
Cdd:pfam00403  1 TFRVSGMHCGGCAAKVEKALSELPGVLSVSVDLATKTVTVTGDAESTKLEKLVEA 55
PRK13748 PRK13748
putative mercuric reductase; Provisional
 24-89 9.16e-11

putative mercuric reductase; Provisional


Pssm-ID: 184298 [Multi-domain]  Cd Length: 561  Bit Score: 56.31  E-value: 9.16e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489242342  24 VTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDkAQPEALTEATANAGYPSTV 89
Cdd:PRK13748   2 TTLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVG-TSPDALTAAVAGLGYRATL 66
UxxU_metal_bind NF041115
metal-binding (seleno)protein; Known members of this family are selenoproteins with an ...
 23-89 1.97e-10

metal-binding (seleno)protein; Known members of this family are selenoproteins with an exceptional UXXU motif, with two selenocysteines. Known members so far derive primarily from MAGs, and have an N-terminal signal peptide N-terminal to the region represented in the seed alignment. Note that this model represents a specific clade of a more widely distributed domain that frequently appears 3 or 4 times in a single protein, so the domain-specific cutoff is critical to identification. Homologous domains, outside the scope of this model, are found in CopZ family copper chaperones and heavy metal-translocating P-type ATPases.


Pssm-ID: 469038 [Multi-domain]  Cd Length: 74  Bit Score: 51.56  E-value: 1.97e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489242342 23 TVTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEATANAGYPSTV 89
Cdd:NF041115  5 TVILAIEGMTUASUPLIAKKALEGLEGVEKADVSYKEGRAEVAFDPDKVSAAQMVDAVNRIGFRASV 71
 
Name Accession Description Interval E-value
MerP TIGR02052
mercuric transport protein periplasmic component; This model represents the periplasmic ...
 1-91 8.40e-24

mercuric transport protein periplasmic component; This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403). [Cellular processes, Detoxification]


Pssm-ID: 131107 [Multi-domain]  Cd Length: 92  Bit Score: 86.24  E-value: 8.40e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489242342   1 MRKLLIAV-LFALPFVALAAPPKTVTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEA 79
Cdd:TIGR02052  1 MKKLATLLaLFVLTSLPAWAATQTVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEA 80

                         90
                 ....*....|..
gi 489242342  80 TANAGYPSTVQK 91
Cdd:TIGR02052 81 TTDAGYPSSLKQ 92
CopZ COG2608
Copper chaperone CopZ [Inorganic ion transport and metabolism];
22-91 2.30e-23

Copper chaperone CopZ [Inorganic ion transport and metabolism];


Pssm-ID: 442020 [Multi-domain]  Cd Length: 71  Bit Score: 84.57  E-value: 2.30e-23
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489242342 22 KTVTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEATANAGYPSTVQK 91
Cdd:COG2608   2 KTVTLKVEGMTCGHCVARVEKALKALDGVASVEVDLATGTATVTYDPEKVSLEDIKAAIEEAGYEVEKAE 71
HMA cd00371
Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid ...
 25-88 9.27e-19

Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.


Pssm-ID: 238219 [Multi-domain]  Cd Length: 63  Bit Score: 72.64  E-value: 9.27e-19
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489242342 25 TLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDkAQPEALTEATANAGYPST 88
Cdd:cd00371   1 ELSVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPE-VSPEELLEAIEDAGYKAR 63
ZntA COG2217
Cation-transporting P-type ATPase [Inorganic ion transport and metabolism];
22-86 1.45e-16

Cation-transporting P-type ATPase [Inorganic ion transport and metabolism];


Pssm-ID: 441819 [Multi-domain]  Cd Length: 717  Bit Score: 72.48  E-value: 1.45e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489242342  22 KTVTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEATANAGYP 86
Cdd:COG2217    1 ERVRLRIEGMTCAACAWLIEKALRKLPGVLSARVNLATERARVEYDPGKVSLEELIAAVEKAGYE 65
HMA pfam00403
Heavy-metal-associated domain;
25-79 4.66e-14

Heavy-metal-associated domain;


Pssm-ID: 459804 [Multi-domain]  Cd Length: 58  Bit Score: 60.33  E-value: 4.66e-14
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 489242342  25 TLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEA 79
Cdd:pfam00403  1 TFRVSGMHCGGCAAKVEKALSELPGVLSVSVDLATKTVTVTGDAESTKLEKLVEA 55
PRK13748 PRK13748
putative mercuric reductase; Provisional
 24-89 9.16e-11

putative mercuric reductase; Provisional


Pssm-ID: 184298 [Multi-domain]  Cd Length: 561  Bit Score: 56.31  E-value: 9.16e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489242342  24 VTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDkAQPEALTEATANAGYPSTV 89
Cdd:PRK13748   2 TTLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVG-TSPDALTAAVAGLGYRATL 66
UxxU_metal_bind NF041115
metal-binding (seleno)protein; Known members of this family are selenoproteins with an ...
 23-89 1.97e-10

metal-binding (seleno)protein; Known members of this family are selenoproteins with an exceptional UXXU motif, with two selenocysteines. Known members so far derive primarily from MAGs, and have an N-terminal signal peptide N-terminal to the region represented in the seed alignment. Note that this model represents a specific clade of a more widely distributed domain that frequently appears 3 or 4 times in a single protein, so the domain-specific cutoff is critical to identification. Homologous domains, outside the scope of this model, are found in CopZ family copper chaperones and heavy metal-translocating P-type ATPases.


Pssm-ID: 469038 [Multi-domain]  Cd Length: 74  Bit Score: 51.56  E-value: 1.97e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489242342 23 TVTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEATANAGYPSTV 89
Cdd:NF041115  5 TVILAIEGMTUASUPLIAKKALEGLEGVEKADVSYKEGRAEVAFDPDKVSAAQMVDAVNRIGFRASV 71
TIGR00003 TIGR00003
copper ion binding protein; This model describes an apparently copper-specific subfamily of ...
 24-85 7.61e-10

copper ion binding protein; This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases. [Transport and binding proteins, Cations and iron carrying compounds]


Pssm-ID: 188014 [Multi-domain]  Cd Length: 66  Bit Score: 50.23  E-value: 7.61e-10
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489242342  24 VTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTYDPDKAQPEALTEATANAGY 85
Cdd:TIGR00003  2 QTFQVKGMSCNHCVDKIEKFVGEIEGVSKVKVQLEKEKVVVEFDAPNVSATEICEAILDAGY 63
copA PRK10671
copper-exporting P-type ATPase CopA;
5-85 1.37e-09

copper-exporting P-type ATPase CopA;


Pssm-ID: 182635 [Multi-domain]  Cd Length: 834  Bit Score: 52.82  E-value: 1.37e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489242342   5 LIAVLFALPfVALAAPPKTVTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQKTATVTydpDKAQPEALTEATANAG 84
Cdd:PRK10671  83 LTAASEELP-AATADDDDSQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVM---GSASPQDLVQAVEKAG 158


                 .
gi 489242342  85 Y 85
Cdd:PRK10671 159 Y 159
copA PRK10671
copper-exporting P-type ATPase CopA;
21-90 5.91e-05

copper-exporting P-type ATPase CopA;


Pssm-ID: 182635 [Multi-domain]  Cd Length: 834  Bit Score: 39.72  E-value: 5.91e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489242342  21 PKTVTLDVQNMTCGLCPITVKKSLEKVSGVSDVQVNFDQktATVTYDpdkAQPEALTEATANAGYPSTVQ 90
Cdd:PRK10671   2 SQTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSITE--AHVTGT---ASAEALIETIKQAGYDASVS 66
 
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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