PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' domains of PDI, ERp72, ERp57 (or ERp60) and EFP1. PDI, ERp72 and ERp57 are endoplasmic reticulum (ER)-resident eukaryotic proteins involved in oxidative protein folding. They are oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. PDI and ERp57 have the abb'a' domain structure (where a and a' are redox active TRX domains while b and b' are redox inactive TRX-like domains). PDI also contains an acidic region (c domain) after the a' domain that is absent in ERp57. ERp72 has an additional a domain at the N-terminus (a"abb'a' domain structure). ERp57 interacts with the lectin chaperones, calnexin and calreticulin, and specifically promotes the oxidative folding of glycoproteins, while PDI shows a wider substrate specificity. ERp72 associates with several ER chaperones and folding factors to form complexes in the ER that bind nascent proteins. EFP1 is a binding partner protein of thyroid oxidase, which is responsible for the generation of hydrogen peroxide, a crucial substrate of thyroperoxidase, which functions to iodinate thyroglobulin and synthesize thyroid hormones.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340 115 VKQLVGKNFNVVVFDKEKDVFVMFYAPWSKKCKMLFPLLEELGRKYQNHSTIIIAKIDVTANDIQLMYL-DRYPFFRLFP 193
Cdd:cd02995    2 VKVVVGKNFDEVVLDSDKDVLVEFYAPWCGHCKALAPIYEELAEKLKGDDNVVIAKMDATANDVPSEFVvDGFPTILFFP 81

                         90       100
                 ....*....|....*....|...
gi 767988340 194 SGS-QQAVLYKGEHTLKGFSDFL 215
Cdd:cd02995   82 AGDkSNPIKYEGDRTLEDLIKFI 104

Thioredoxin-like domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340    3 HMLLFVSKSSESYGIIIQHYKLASKEFQNKILFILVDADepRNGRVFKYFRVTEVDIPSVQILNLSSDARYKMPSDDITY 82
Cdd:pfam13848  98 LLLLFLKKDDESTEEFKKALEKVAKKFRGKINFALVDAK--SFGRPLEYFGLSESDLPVIVIVDSFSHMYKYFPSDEFSP 175

                  ....*.
gi 767988340   83 ESLKKF 88
Cdd:pfam13848 176 ESLKEF 181

PDIa family, C-terminal TRX domain (a') subfamily; composed of the C-terminal redox active a' domains of PDI, ERp72, ERp57 (or ERp60) and EFP1. PDI, ERp72 and ERp57 are endoplasmic reticulum (ER)-resident eukaryotic proteins involved in oxidative protein folding. They are oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. PDI and ERp57 have the abb'a' domain structure (where a and a' are redox active TRX domains while b and b' are redox inactive TRX-like domains). PDI also contains an acidic region (c domain) after the a' domain that is absent in ERp57. ERp72 has an additional a domain at the N-terminus (a"abb'a' domain structure). ERp57 interacts with the lectin chaperones, calnexin and calreticulin, and specifically promotes the oxidative folding of glycoproteins, while PDI shows a wider substrate specificity. ERp72 associates with several ER chaperones and folding factors to form complexes in the ER that bind nascent proteins. EFP1 is a binding partner protein of thyroid oxidase, which is responsible for the generation of hydrogen peroxide, a crucial substrate of thyroperoxidase, which functions to iodinate thyroglobulin and synthesize thyroid hormones.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340 115 VKQLVGKNFNVVVFDKEKDVFVMFYAPWSKKCKMLFPLLEELGRKYQNHSTIIIAKIDVTANDIQLMYL-DRYPFFRLFP 193
Cdd:cd02995    2 VKVVVGKNFDEVVLDSDKDVLVEFYAPWCGHCKALAPIYEELAEKLKGDDNVVIAKMDATANDVPSEFVvDGFPTILFFP 81

                         90       100
                 ....*....|....*....|...
gi 767988340 194 SGS-QQAVLYKGEHTLKGFSDFL 215
Cdd:cd02995   82 AGDkSNPIKYEGDRTLEDLIKFI 104

Protein Disulfide Isomerase (PDIa) family, redox active TRX domains; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI and PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5, PDIR, ERp46 and the transmembrane PDIs. PDI, ERp57, ERp72, P5, PDIR and ERp46 are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins usually contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and may also contain one or more redox inactive TRX-like (b) domains. Only one a domain is required for the oxidase function but multiple copies are necessary for the isomerase function. The different types of PDIs may show different substrate specificities and tissue-specific expression, or may be induced by stress. PDIs are in their reduced form at steady state and are oxidized to the active form by Ero1, which is localized in the ER through ERp44. Some members of this family also contain a DnaJ domain in addition to the redox active a domains; examples are ERdj5 and Pfj2. Also included in the family is the redox inactive N-terminal TRX-like domain of ERp29.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340 116 KQLVGKNFNVVVFDkEKDVFVMFYAPWSKKCKMLFPLLEELGRKYQNHSTIIIAKIDVTAN-DI-QLMYLDRYPFFRLFP 193
Cdd:cd02961    1 VELTDDNFDELVKD-SKDVLVEFYAPWCGHCKALAPEYEKLAKELKGDGKVVVAKVDCTANnDLcSEYGVRGYPTIKLFP 79

                         90       100
                 ....*....|....*....|..
gi 767988340 194 SGSQQAVLYKGEHTLKGFSDFL 215
Cdd:cd02961   80 NGSKEPVKYEGPRTLESLVEFI 101

Protein Disulfide Isomerase (PDIb') family, redox inactive TRX-like domain b'; composed of eukaryotic proteins involved in oxidative protein folding in the endoplasmic reticulum (ER) by acting as catalysts and folding assistants. Members of this family include PDI, calsequestrin and other PDI-related proteins like ERp72, ERp57 (or ERp60), ERp44, P5 and PDIR. PDI, ERp57, ERp72, P5 and PDIR are all oxidases, catalyzing the formation of disulfide bonds of newly synthesized polypeptides in the ER. They also exhibit reductase activity in acting as isomerases to correct any non-native disulfide bonds, as well as chaperone activity to prevent protein aggregation and facilitate the folding of newly synthesized proteins. These proteins contain multiple copies of a redox active TRX (a) domain containing a CXXC motif, and one or more redox inactive TRX-like (b) domains. The molecular structure of PDI is abb'a'. Also included in this family is the PDI-related protein ERp27, which contains only redox-inactive TRX-like (b and b') domains. The redox inactive domains are implicated in substrate recognition with the b' domain serving as the primary substrate binding site. Only the b' domain is necessary for the binding of small peptide substrates. In addition to the b' domain, other domains are required for the binding of larger polypeptide substrates. The b' domain is also implicated in chaperone activity.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340   1 MSHMLLFVSKSSESYGIIIQHYKLASKEFQNKILFILVDADEprNGRVFKYFRVTEVDIPSVQILNLSSDARYKMPSDDI 80
Cdd:cd02982   13 KPLLVLFYNKDDSESEELRERFKEVAKKFKGKLLFVVVDADD--FGRHLEYFGLKEEDLPVIAIINLSDGKKYLMPEEEL 90

                         90
                 ....*....|...
gi 767988340  81 TYESLKKFGRSFL 93
Cdd:cd02982   91 TAESLEEFVEDFL 103

PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340 115 VKQLVGKNFNVVVfdKEKDVFVMFYAPWSKKCKMLFPLLEELGRKYQNHST-IIIAKIDVTA-----NDIQlmyLDRYPF 188
Cdd:cd03005    2 VLELTEDNFDHHI--AEGNHFVKFFAPWCGHCKRLAPTWEQLAKKFNNENPsVKIAKVDCTQhrelcSEFQ---VRGYPT 76

                         90       100
                 ....*....|....*....|....*..
gi 767988340 189 FRLFPSGsQQAVLYKGEHTLKGFSDFL 215
Cdd:cd03005   77 LLLFKDG-EKVDKYKGTRDLDSLKEFV 102

Chaperedoxin CnoX, contains thioredoxin-like and TPR-like domains, YbbN/TrxSC family [Posttranslational modification, protein turnover, chaperones];

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767988340 115 VKQLVGKNFNVVVFDKEKDVFVMFYAPWSKKCKMLFPLLEELGRKYQNHstIIIAKIDVTAN 176
Cdd:COG3118    2 VVELTDENFEEEVLESDKPVLVDFWAPWCGPCKMLAPVLEELAAEYGGK--VKFVKVDVDEN 61

PDI family, MPD1-like subfamily; composed of eukaryotic proteins similar to Saccharomyces cerevisiae MPD1 protein, which contains a single redox active TRX domain located at the N-terminus, and an ER retention signal at the C-terminus indicative of an ER-resident protein. MPD1 has been shown to suppress the maturation defect of carboxypeptidase Y caused by deletion of the yeast PDI1 gene. Other characterized members of this subfamily include the Aspergillus niger prpA protein and Giardia PDI-1. PrpA is non-essential to strain viability, however, its transcript level is induced by heterologous protein expression suggesting a possible role in oxidative protein folding during high protein production. Giardia PDI-1 has the ability to refold scrambled RNase and exhibits transglutaminase activity.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340 115 VKQLVGKNFNVVVFDKEKDVFVMFYAPWSKKCKMLFPLLEELGRkyQNHSTIIIAKIDVTAN---------DIQlmyldR 185
Cdd:cd03002    2 VYELTPKNFDKVVHNTNYTTLVEFYAPWCGHCKNLKPEYAKAAK--ELDGLVQVAAVDCDEDknkplcgkyGVQ-----G 74

                         90       100       110
                 ....*....|....*....|....*....|...
gi 767988340 186 YPFFRLFPSG---SQQAVL-YKGEHTLKGFSDF 214
Cdd:cd03002   75 FPTLKVFRPPkkaSKHAVEdYNGERSAKAIVDF 107

PDIa family, P5 subfamily; composed of eukaryotic proteins similar to human P5, a PDI-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. Some members of this subfamily are P5-like proteins containing only one redox active TRX domain.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340 115 VKQLVGKNFNVVVFDKEKDVFVMFYAPWSKKCKMLFPLLEELGRKYQnhSTIIIAKIDVTANDiQLM--YLDR-YPFFRL 191
Cdd:cd03001    2 VVELTDSNFDKKVLNSDDVWLVEFYAPWCGHCKNLAPEWKKAAKALK--GIVKVGAVDADVHQ-SLAqqYGVRgFPTIKV 78

                         90       100
                 ....*....|....*....|...
gi 767988340 192 FPSGSQQAVLYKGEHTLKGFSDF 214
Cdd:cd03001   79 FGAGKNSPQDYQGGRTAKAIVSA 101

TRX family; composed of two groups: Group I, which includes proteins that exclusively encode a TRX domain; and Group II, which are composed of fusion proteins of TRX and additional domains. Group I TRX is a small ancient protein that alter the redox state of target proteins via the reversible oxidation of an active site dithiol, present in a CXXC motif, partially exposed at the protein's surface. TRX reduces protein disulfide bonds, resulting in a disulfide bond at its active site. Oxidized TRX is converted to the active form by TRX reductase, using reducing equivalents derived from either NADPH or ferredoxins. By altering their redox state, TRX regulates the functions of at least 30 target proteins, some of which are enzymes and transcription factors. It also plays an important role in the defense against oxidative stress by directly reducing hydrogen peroxide and certain radicals, and by serving as a reductant for peroxiredoxins. At least two major types of functional TRXs have been reported in most organisms; in eukaryotes, they are located in the cytoplasm and the mitochondria. Higher plants contain more types (at least 20 TRX genes have been detected in the genome of Arabidopsis thaliana), two of which (types f amd m) are located in the same compartment, the chloroplast. Also included in the alignment are TRX-like domains which show sequence homology to TRX but do not contain the redox active CXXC motif. Group II proteins, in addition to either a redox active TRX or a TRX-like domain, also contain additional domains, which may or may not possess homology to known proteins.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 767988340 129 DKEKDVFVMFYAPWSKKCKMLFPLLEELGRKYQNhstIIIAKIDVTAN 176
Cdd:cd02947    8 KSAKPVVVDFWAPWCGPCKAIAPVLEELAEEYPK---VKFVKVDVDEN 52

ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 767988340 122 NFN-VVVFDKEKDVFVMFYAPWSKKCKMLFPLLEELGRKYQnhSTIIIAKIDVTAN 176
Cdd:cd02956    2 NFQqVLQESTQVPVVVDFWAPRSPPSKELLPLLERLAEEYQ--GQFVLAKVNCDAQ 55

PDIa family, TMX subfamily; composed of proteins similar to the TRX-related human transmembrane protein, TMX. TMX is a type I integral membrane protein; the N-terminal redox active TRX domain is present in the endoplasmic reticulum (ER) lumen while the C-terminus is oriented towards the cytoplasm. It is expressed in many cell types and its active site motif (CPAC) is unique. In vitro, TMX reduces interchain disulfides of insulin and renatures inactive RNase containing incorrect disulfide bonds. The C. elegans homolog, DPY-11, is expressed only in the hypodermis and resides in the cytoplasm. It is required for body and sensory organ morphogeneis. Another uncharacterized TRX-related transmembrane protein, human TMX4, is included in the alignment. The active site sequence of TMX4 is CPSC.

                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 767988340 136 VMFYAPWSKKCKMLFPLLEELGRKYQNHStIIIAKIDVTAN 176
Cdd:cd02994   21 IEFYAPWCPACQQLQPEWEEFADWSDDLG-INVAKVDVTQE 60

disulphide isomerase; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340 115 VKQLVGKNFNVvvFDKEKD-VFVMFYAPWSKKCKMLFPLLEELGRKYQNH-STIIIAKIDVTAND--IQLMYLDRYPFFR 190
Cdd:PTZ00102  34 VTVLTDSTFDK--FITENEiVLVKFYAPWCGHCKRLAPEYKKAAKMLKEKkSEIVLASVDATEEMelAQEFGVRGYPTIK 111

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 767988340 191 LFPSGSQqaVLYKGEHTLKGFSDFLESHIK---TKIEDEDELLSVEQN 235
Cdd:PTZ00102 112 FFNKGNP--VNYSGGRTADGIVSWIKKLTGpavTEVESASEIKLIAKK 157

PDIa family, 5'-Adenylylsulfate (APS) reductase subfamily; composed of plant-type APS reductases containing a C-terminal redox active TRX domain and an N-terminal reductase domain which is part of a superfamily that includes N type ATP PPases. APS reductase catalyzes the reduction of activated sulfate to sulfite, a key step in the biosynthesis of sulfur-containing metabolites. Sulfate is first activated by ATP sulfurylase, forming APS, which can be phosphorylated to 3'-phosphoadenosine-5'-phosphosulfate (PAPS). Depending on the organism, either APS or PAPS can be used for sulfate reduction. Prokaryotes and fungi use PAPS, whereas plants use both APS and PAPS. Since plant-type APS reductase uses glutathione (GSH) as its electron donor, the C-terminal domain may function like glutaredoxin, a GSH-dependent member of the TRX superfamily. The flow of reducing equivalents goes from GSH -> C-terminal TRX domain -> N-terminal reductase domain -> APS. Plant-type APS reductase shows no homology to that of dissimilatory sulfate-reducing bacteria, which is an iron-sulfur flavoenzyme. Also included in the alignment is EYE2 from Chlamydomonas reinhardtii, a protein required for eyespot assembly.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340 130 KEKDVFVMFYAPWSKKCKMLFPLLEELGRKYQNHStIIIAKIDVTAND----IQLMYLDRYPFFRLFPSGSQQAVLYKGE 205
Cdd:cd02993   20 RNQSTLVVLYAPWCPFCQAMEASYEELAEKLAGSN-VKVAKFNADGEQrefaKEELQLKSFPTILFFPKNSRQPIKYPSE 98

thioredoxin; Provisional

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767988340 134 VFVMFYAPWSKKCKMLFPLLEELGRKYQNhstIIIAKIDV--TANDIQLMYLDRYPFFRLFPSGSQQAVL 201
Cdd:PTZ00051  21 VIVDFYAEWCGPCKRIAPFYEECSKEYTK---MVFVKVDVdeLSEVAEKENITSMPTFKVFKNGSVVDTL 87