Zinc peptidases M18, M20, M28, and M42; Zinc peptidases play vital roles in metabolic and signaling pathways throughout all kingdoms of life. This hierarchy contains zinc peptidases that correspond to the MH clan in the MEROPS database, which contains 4 families (M18, M20, M28, M42). The peptidase M20 family includes carboxypeptidases such as the glutamate carboxypeptidase from Pseudomonas, the thermostable carboxypeptidase Ss1 of broad specificity from archaea and yeast Gly-X carboxypeptidase. The dipeptidases include bacterial dipeptidase, peptidase V (PepV), a non-specific eukaryotic dipeptidase, and two Xaa-His dipeptidases (carnosinases). There is also the bacterial aminopeptidase, peptidase T (PepT) that acts only on tripeptide substrates and has therefore been termed a tripeptidase. Peptidase family M28 contains aminopeptidases and carboxypeptidases, and has co-catalytic zinc ions. However, several enzymes in this family utilize other first row transition metal ions such as cobalt and manganese. Each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Glutamate carboxypeptidase II and plasma glutamate carboxypeptidase hydrolyze dipeptides. Peptidase families M18 and M42 contain metallo-aminopeptidases. M18 is widely distributed in bacteria and eukaryotes. However, only yeast aminopeptidase I and mammalian aspartyl aminopeptidase have been characterized in detail. Some M42 (also known as glutamyl aminopeptidase) enzymes exhibit aminopeptidase specificity while others also have acylaminoacyl-peptidase activity (i.e. hydrolysis of acylated N-terminal residues).

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 437 KTVTNVVGFVMGLTSPDRYIIVGSHHHTAHsYNGQEWASSTAIITAFIRALMSKVKR-GWRPDRTIVFCSWGGTAFGNIG 515
Cdd:cd03874   55 SPITNVVGKIEGIEQPDRAIIIGAHRDSWG-YGAGYPNSGTAVLLEIARLFQQLKKKfGWKPLRTIYFISWDGSEFGLAG 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 516 SYEWGEDFKKVLQKNVVAYISLHSPIRGNSSLYPVASPSLQQLVVEKNNFNCTRRAQ-----CPETNISSIQIQGDADYF 590
Cdd:cd03874  134 STELGEDRKASLKDEVYAYINIDQLVIGNSELDVDAHPLLQSLFRKASKKVKFPGNEdwwkhSPNAKVSNLHQYGDWTPF 213

                        170
                 ....*....|....*...
gi 767926205 591 INHLGVPIVQFAYEDIKT 608
Cdd:cd03874  214 LNHLGIPVAVFSFKNDRN 231

M28 Zn-peptidase Transferrin Receptor-like family; Peptidase M28 family; Transferrin Receptor (TfR) and prostate-specific membrane antigen (PSMA, also called glutamate carboxypeptidase or GCP-II) subfamily. TfR and PSMA are homodimeric type II transmembrane proteins containing three distinct domains: protease-like, apical or protease-associated (PA) and helical domains. The protease-like domain is a large extracellular portion (ectodomain). In TfR, it contains a binding site for the transferrin molecule and has 28% identity to membrane glutamate carboxypeptidase II (mGCP-II or PSMA). The PA domain is inserted between the first and second strands of the central beta sheet in the protease-like domain. TfR1 is widely expressed, and is a key player in the uptake of iron-loaded transferrin (Tf) into cells. The TfR1 homodimer binds two molecules of Tf and the complex is then internalized. TfR1 may also participate in cell growth and proliferation. TfR2 binds Tf but with a significantly lower affinity than TfR1. It is expressed chiefly in hepatocytes, hematopoietic cells, and duodenal crypt cells; its expression overlaps with that of hereditary hemochromatosis protein (HFE). TfR2 is involved in iron homeostasis; in humans, mutations in TfR2 are associated with a form of hemochromatosis (HFE3). PSMA is over-expressed predominantly in prostate cancer (PCa) as well as in the neovasculature of most solid tumors, but not in the vasculature of normal tissues. PSMA is considered a biomarker for PCa and possibly for use as an imaging and therapeutic target. The extracellular domain of PSMA possesses two unique enzymatic functions: N-acetylated, alpha-linked acidic dipeptidase (NAALADase) which cleaves terminal glutamate from the neurodipeptide N-acetyl-aspartyl-glutamate (NAAG), and folate hydrolase (FOLH) which cleaves the terminal glutamates from gamma-linked polyglutamates (carboxypeptidase). A mutation in this gene may be associated with impaired intestinal absorption of dietary folates, resulting in low blood folate levels and consequent hyperhomocysteinemia. Expression of this protein in the brain may be involved in a number of pathological conditions associated with glutamate excitotoxicity. This gene likely arose from a duplication event of a nearby chromosomal region. Alternative splicing gives rise to multiple transcript variants. While related in sequence to peptidase M28 GCP-II, TfR lacks the metal ion coordination centers and protease activity.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 437 KTVTNVVGFVMGLTSPDRYIIVGSHHHTAHsYNGQEWASSTAIITAFIRALMSKVKR-GWRPDRTIVFCSWGGTAFGNIG 515
Cdd:cd03874   55 SPITNVVGKIEGIEQPDRAIIIGAHRDSWG-YGAGYPNSGTAVLLEIARLFQQLKKKfGWKPLRTIYFISWDGSEFGLAG 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 516 SYEWGEDFKKVLQKNVVAYISLHSPIRGNSSLYPVASPSLQQLVVEKNNFNCTRRAQ-----CPETNISSIQIQGDADYF 590
Cdd:cd03874  134 STELGEDRKASLKDEVYAYINIDQLVIGNSELDVDAHPLLQSLFRKASKKVKFPGNEdwwkhSPNAKVSNLHQYGDWTPF 213

                        170
                 ....*....|....*...
gi 767926205 591 INHLGVPIVQFAYEDIKT 608
Cdd:cd03874  214 LNHLGIPVAVFSFKNDRN 231

Peptidase family M28;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205  441 NVVGFVMGlTSPDRYIIVGSHH-HTAHSY----NgqewASSTAIITAFIRALmskvKRGWRPDRTIVFCSWGGTAFGNIG 515
Cdd:pfam04389   1 NVIAKLPG-KAPDEVVLLSAHYdSVGTGPgaddN----ASGVAALLELARVL----AAGQRPKRSVRFLFFDAEEAGLLG 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205  516 SYEWGEdfKKVLQKNVVAYISLHSPIRGNSSLYPVASP----SLQQLVVEKNNFNCTRRAQCPETNISsiqIQGDADYFI 591
Cdd:pfam04389  72 SHHFAK--SHPPLKKIRAVINLDMIGSGGPALLFQSGPkgssLLEKYLKAAAKPYGVTLAEDPFQERG---GPGRSDHAP 146

                         170
                  ....*....|....*
gi 767926205  592 -NHLGVPIVQFAYED 605
Cdd:pfam04389 147 fIKAGIPGLDLAFTD 161

M28 Zn-peptidase Transferrin Receptor-like family; Peptidase M28 family; Transferrin Receptor (TfR) and prostate-specific membrane antigen (PSMA, also called glutamate carboxypeptidase or GCP-II) subfamily. TfR and PSMA are homodimeric type II transmembrane proteins containing three distinct domains: protease-like, apical or protease-associated (PA) and helical domains. The protease-like domain is a large extracellular portion (ectodomain). In TfR, it contains a binding site for the transferrin molecule and has 28% identity to membrane glutamate carboxypeptidase II (mGCP-II or PSMA). The PA domain is inserted between the first and second strands of the central beta sheet in the protease-like domain. TfR1 is widely expressed, and is a key player in the uptake of iron-loaded transferrin (Tf) into cells. The TfR1 homodimer binds two molecules of Tf and the complex is then internalized. TfR1 may also participate in cell growth and proliferation. TfR2 binds Tf but with a significantly lower affinity than TfR1. It is expressed chiefly in hepatocytes, hematopoietic cells, and duodenal crypt cells; its expression overlaps with that of hereditary hemochromatosis protein (HFE). TfR2 is involved in iron homeostasis; in humans, mutations in TfR2 are associated with a form of hemochromatosis (HFE3). PSMA is over-expressed predominantly in prostate cancer (PCa) as well as in the neovasculature of most solid tumors, but not in the vasculature of normal tissues. PSMA is considered a biomarker for PCa and possibly for use as an imaging and therapeutic target. The extracellular domain of PSMA possesses two unique enzymatic functions: N-acetylated, alpha-linked acidic dipeptidase (NAALADase) which cleaves terminal glutamate from the neurodipeptide N-acetyl-aspartyl-glutamate (NAAG), and folate hydrolase (FOLH) which cleaves the terminal glutamates from gamma-linked polyglutamates (carboxypeptidase). A mutation in this gene may be associated with impaired intestinal absorption of dietary folates, resulting in low blood folate levels and consequent hyperhomocysteinemia. Expression of this protein in the brain may be involved in a number of pathological conditions associated with glutamate excitotoxicity. This gene likely arose from a duplication event of a nearby chromosomal region. Alternative splicing gives rise to multiple transcript variants. While related in sequence to peptidase M28 GCP-II, TfR lacks the metal ion coordination centers and protease activity.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 437 KTVTNVVGFVMGLTSPDRYIIVGSHHHTAHsYNGQEWASSTAIITAFIRALMSKVKR-GWRPDRTIVFCSWGGTAFGNIG 515
Cdd:cd03874   55 SPITNVVGKIEGIEQPDRAIIIGAHRDSWG-YGAGYPNSGTAVLLEIARLFQQLKKKfGWKPLRTIYFISWDGSEFGLAG 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 516 SYEWGEDFKKVLQKNVVAYISLHSPIRGNSSLYPVASPSLQQLVVEKNNFNCTRRAQ-----CPETNISSIQIQGDADYF 590
Cdd:cd03874  134 STELGEDRKASLKDEVYAYINIDQLVIGNSELDVDAHPLLQSLFRKASKKVKFPGNEdwwkhSPNAKVSNLHQYGDWTPF 213

                        170
                 ....*....|....*...
gi 767926205 591 INHLGVPIVQFAYEDIKT 608
Cdd:cd03874  214 LNHLGIPVAVFSFKNDRN 231

M28 Zn-peptidase Transferrin Receptor family; Peptidase M28 family; Transferrin Receptor (TfR) subfamily. TfRs are homodimeric type II transmembrane proteins containing three distinct domains: protease-like, apical or protease-associated (PA), and helical domains. The protease-like domain is a large extracellular portion (ectodomain). In TfR, it contains a binding site for the transferrin molecule and has 28% identity to membrane glutamate carboxypeptidase II (mGCP-II or PSMA). The PA domain is inserted between the first and second strands of the central beta sheet in the protease-like domain. TfR1 is widely expressed, and is a key player in the uptake of iron-loaded transferrin (Tf) into cells. The TfR1 homodimer binds two molecules of Tf and the complex is then internalized. TfR1 may also participate in cell growth and proliferation. TfR2 binds Tf but with a significantly lower affinity than TfR1. It is expressed chiefly in hepatocytes, hematopoietic cells, and duodenal crypt cells; its expression overlaps with that of hereditary hemochromatosis protein (HFE). TfR2 is involved in iron homeostasis; in humans, mutations in TfR2 are associated with a form of hemochromatosis (HFE3). While related in sequence to peptidase M28 glutamate carboxypeptidase II (also called prostate-specific membrane antigen or PSMA), TfR lacks the metal ion coordination centers and protease activity of that group.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 441 NVVGFVMGLTSPDRYIIVGSHHHT-----AHSYNGqewassTAIITAFIRALMSKVK-RGWRPDRTIVFCSWGGTAFGNI 514
Cdd:cd09848   58 NIFGVIKGFVEPDRYVVIGAQRDAwgpgaAKSGVG------TALLLELARTFSDMVKnDGFKPRRSIVFASWSAGDFGSV 131

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 515 GSYEWGEDFKKVLQKNVVAYISLHSPIRGNSSLYPVASPSLQQLV----------VEKNNFNCTRRAQCPETNISSIQIQ 584
Cdd:cd09848  132 GATEWLEGYLSSLHLKAFTYISLDGAVLGDDSFKASASPLLYTLIestmkqvkspVHSGQSYYETRSSWWASIVEPLGLD 211

                        170       180
                 ....*....|....*....|
gi 767926205 585 GDADYFINHLGVPIVQFAYE 604
Cdd:cd09848  212 SAAYPFLAFSGIPSVSFHFT 231

PA_TfR: Protease-associated domain containing proteins like transferrin receptor (TfR). This group contains various PA domain-containing proteins similar to human TfR1 and TfR2. TfR1 and TfR2 are type II membrane proteins, belonging to the peptidase M28 family. TfR1 is homodimeric, widely expressed, and a key player in the uptake of iron-loaded transferrin (Tf) into cells. The TfR1 homodimer binds two molecules of Tf and this complex is internalized. In addition to its role in iron uptake, TfR1 may participate in cell growth and proliferation. TfR2 also binds Tf but with a significantly lower affinity than does TfR1. TfR2 is expressed chiefly in hepatocytes, hematopoietic cells, and duodenal crypt cells; its expression overlaps with that of hereditary hemochromatosis protein (HFE). TfR2 is involved in iron homeostasis. HFE and TfR2 interact in cells. By one model for serum iron sensing, at low or basal iron concentrations, HFE and TFR1 form a complex at the plasma membrane; at increased Tf, Tf competes with HFE for binding of TfR1, resulting in HFE disassociating from TfR1 and associating with TfR2 . The TfR1-TfR2 association might initiate a signal cascade leading to the induction of hepcidin (a small peptide hormone that controls systemic iron levels). Human mutations in TfR2 are associated with a form of hemochromatosis (HFE3). The significance of the PA domain to TfRs has not been ascertained. It may be a protein-protein interaction domain. At peptidase active sites, the PA domain may participate in substrate binding and/or promoting conformational changes, which influence the stability and accessibility of the site to substrate.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 273 YAAYSAKGTLKAEVIDVSYGMADDLKRIRKIK-NVTNQIALLKLGKLPLLYKLSSLEKAGFGGVLLYIDPCDLPKTvnPS 351
Cdd:cd02128   20 YVAYSAAGTVTGKLVYANYGRKKDFEDLQSVGvSVNGSVVLVRAGKISFAEKVANAEKLGAVGVLIYPDPADFPID--PS 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 767926205 352 HDTFMVSLNPG-GDPSTPGYPSVDES-FRQSRSN-LTSLLVQPISAPLVAKLIS 402
Cdd:cd02128   98 ETALFGHVHLGtGDPYTPGFPSFNHTqFPPSQSSgLPNIPAQTISAAAAAKLLS 151

M28 Zn-peptidases include aminopeptidases and carboxypeptidases; Peptidase M28 family (also called aminopeptidase Y family) contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. The aminopeptidases in this family are also called bacterial leucyl aminopeptidases, but are able to release a variety of N-terminal amino acids. IAP aminopeptidase and aminopeptidase Y preferentially release basic amino acids while glutamate carboxypeptidase II preferentially releases C-terminal glutamates. Plasma glutamate carboxypeptidase (PGCP) and glutamate carboxypeptidase II (NAALADase) hydrolyze dipeptides. Several members of the M28 peptidase family have PA domain inserts which may participate in substrate binding and/or in promoting conformational changes, which influence the stability and accessibility of the site to substrate. These include prostate-specific membrane antigen (PSMA), yeast aminopeptidase S (SGAP), human transferrin receptors (TfR1 and TfR2), plasma glutamate carboxypeptidase (PGCP) and several predicted aminopeptidases where relatively little is known about them. Also included in the M28 family are glutaminyl cyclases (QC), which are involved in N-terminal glutamine cyclization of many endocrine peptides. Nicastrin and nicalin belong to this family but lack the amino-acid conservation required for catalytically active aminopeptidases.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 440 TNVVGFVMGLTSPDRYIIVGSHH-HTAHSYNGQEWASSTAIITAFIRALmSKVKRgwRPDRTIVFCSWGGTAFGNIGSYE 518
Cdd:cd02690    2 YNVIATIKGSDKPDEVILIGAHYdSVPLSPGANDNASGVAVLLELARVL-SKLQL--KPKRSIRFAFWDAEELGLLGSKY 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 767926205 519 WGEDFkKVLQKNVVAYISLHSPIRGNSSLY----PVASPSLQQLV 559
Cdd:cd02690   79 YAEQL-LSSLKNIRAALNLDMIGGAGPDLYlqtaPGNDALVEKLL 122

M28 Zn-peptidase, many containing a protease-associated (PA) domain insert; Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized proteins, many of which contain a protease-associated (PA) domain insert which may participate in substrate binding and/or promote conformational changes, influencing the stability and accessibility of the site to substrate. Some proteins in this subfamily are also associated with the PDZ domain, a widespread protein module that has been recruited to serve multiple functions during the course of evolution.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 441 NVVGFVMGLTSPDRYIIVGSH--HHTAHS-------YNG-QEWASSTAIITAFIRALMSKVKrgwrPDRTIVFCSWGGTA 510
Cdd:cd03877    3 NVVGVLEGSDLPDETIVIGAHydHLGIGGgdsgdkiYNGaDDNASGVAAVLELARYFAKQKT----PKRSIVFAAFTAEE 78

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 511 FGNIGSYEWGEDFKKVLqKNVVAYISLH--SPIRGNSSLYPV--ASPSLQQLVVEKNNFN 566
Cdd:cd03877   79 KGLLGSKYFAENPKFPL-DKIVAMLNLDmiGRLGRSKDVYLIgsGSSELENLLKKANKAA 137

M28 Zn-peptidase containing a protease-associated (PA) domain insert; Peptidase family M28 (also called aminopeptidase Y family), uncharacterized subfamily. The M28 family contains aminopeptidases as well as carboxypeptidases. They have co-catalytic zinc ions; each zinc ion is tetrahedrally co-ordinated, with three amino acid ligands plus activated water; one aspartate residue binds both metal ions. This subfamily is composed of uncharacterized proteins containing a protease-associated (PA) domain insert which may participate in substrate binding and/or promote conformational changes, influencing the stability and accessibility of the site to substrate.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767926205 430 VQTVTKLKTVT--NVVGFVMGLTSPDRYIIVGSH--HHTAHS-------YNGQ-EWASSTAIITAFIRALMSKVKrgwRP 497
Cdd:cd05660   48 VPLVSKIEYSTshNVVAILPGSKLPDEYIVLSAHwdHLGIGPpiggdeiYNGAvDNASGVAAVLELARVFAAQDQ---RP 124

                         90
                 ....*....|....*....
gi 767926205 498 DRTIVFCSWGGTAFGNIGS 516
Cdd:cd05660  125 KRSIVFLAVTAEEKGLLGS 143