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Conserved domains on  [gi|1958774364|ref|XP_038965072|]
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procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 isoform X1 [Rattus norvegicus]

Protein Classification

prolyl hydroxylase family protein( domain architecture ID 10653727)

prolyl hydroxylase family protein similar to prolyl 3-hydroxylase 1, a member of the 2-oxoglutarate dioxygenase superfamily, plays a crucial role in collagen synthesis, folding, and assembly

CATH:  2.60.120.620
Gene Ontology:  GO:0008198|GO:0016705

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P4Hc smart00702
Prolyl 4-hydroxylase alpha subunit homologues; Mammalian enzymes catalyse hydroxylation of ...
 340-503 1.79e-25

Prolyl 4-hydroxylase alpha subunit homologues; Mammalian enzymes catalyse hydroxylation of collagen, for example. Prokaryotic enzymes might catalyse hydroxylation of antibiotic peptides. These are 2-oxoglutarate-dependent dioxygenases, requiring 2-oxoglutarate and dioxygen as cosubstrates and ferrous iron as a cofactor.


:

Pssm-ID: 214780  Cd Length: 165  Bit Score: 102.47  E-value: 1.79e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958774364  340 TEVACDELVEEMEHYGqWSLGDNKDNRIQGgyenvPTIDIHMNQITFeREWHK--FLVEYIAPLTEKLYPGYY-TKAQFD 416
Cdd:smart00702   1 SPAECQKLLEEAEPLG-WRGEVTRGIGNPN-----ETSQYRQSNGTW-LELLErdLVIERIRQRLADFLGLLAgLPLSAE 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958774364  417 LAFVVRYKPDeqPSLMPHHDAS-----TFTINIALNrvgEDYEGGGCRFLR---YNCSVRAPRKGWALMHP-GRLTHYHE 487
Cdd:smart00702  74 DAQVARYGPG--GHYGPHVDNFlygdrIATFILYLN---DVEEGGELVFPGlrlMVVATVKPKKGDLLFFPsGHGRSLHG 148

                          170
                   ....*....|....*.
gi 1958774364  488 GLPTTKGTRYIAVSFV 503
Cdd:smart00702 149 VCPVTRGSRWAITGWI 164
GT_LH super family cl45890
catalytic glycosyltransferase (GT) domain found in the lysyl hydroxylase (LH) family; The ...
 1-32 5.37e-16

catalytic glycosyltransferase (GT) domain found in the lysyl hydroxylase (LH) family; The lysyl hydroxylase (LH) family includes LH1-3. LH1 (EC 1.14.11.4, also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 or PLOD1) and LH2 (EC 1.14.11.4, also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 or PLOD2) form hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines may serve as sites of attachment for carbohydrate units and are essential for stability of the intermolecular collagen cross-links. LH1 is part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linking of collagen fibrils. LH3 (EC 1.14.11.4/EC 2.4.1.50/EC 2.4.1.66), also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 (PLOD3), or multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3, is a multifunctional enzyme that catalyzes a series of essential post-translational modifications on Lys residues in procollagen. It converts collagen lysines into 1,2-glucosylgalactosyl-5-hydroxylysines through three consecutive reactions: hydroxylation of collagen lysines (LH activity), N-linked conjugation of galactose to hydroxylysines (GT activity), and conjugation of glucose to galactosyl-5-hydroxylysines (GGT activity). LH3 monomer encompasses three domains; the first two N-terminal domains (catalytic glycosyltransferase domain and accessory domain) show Rossmann-fold architectures reminiscent of glycosyltransferases, whereas the C-terminal domain is characterized by a double-stranded beta-helix (DSBH) fold, highly conserved among the 2-oxoglutarate, Fe2+-dependent dioxygenases. This model corresponds to the N-terminal catalytic glycosyltransferase (GT) domain, which is solely responsible for glycosyltransferase activities (both GT and GGT).


The actual alignment was detected with superfamily member cd23004:

Pssm-ID: 459235  Cd Length: 230  Bit Score: 77.15  E-value: 5.37e-16
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1958774364   1 MGHVRARNLAYDTLPVVIHGNGPTKLQVNYLG 32
Cdd:cd23004   199 DGRVRARNLLYDTLPVIIHGNGPTKLQLNYLG 230
 
Name Accession Description Interval E-value
P4Hc smart00702
Prolyl 4-hydroxylase alpha subunit homologues; Mammalian enzymes catalyse hydroxylation of ...
 340-503 1.79e-25

Prolyl 4-hydroxylase alpha subunit homologues; Mammalian enzymes catalyse hydroxylation of collagen, for example. Prokaryotic enzymes might catalyse hydroxylation of antibiotic peptides. These are 2-oxoglutarate-dependent dioxygenases, requiring 2-oxoglutarate and dioxygen as cosubstrates and ferrous iron as a cofactor.


Pssm-ID: 214780  Cd Length: 165  Bit Score: 102.47  E-value: 1.79e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958774364  340 TEVACDELVEEMEHYGqWSLGDNKDNRIQGgyenvPTIDIHMNQITFeREWHK--FLVEYIAPLTEKLYPGYY-TKAQFD 416
Cdd:smart00702   1 SPAECQKLLEEAEPLG-WRGEVTRGIGNPN-----ETSQYRQSNGTW-LELLErdLVIERIRQRLADFLGLLAgLPLSAE 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958774364  417 LAFVVRYKPDeqPSLMPHHDAS-----TFTINIALNrvgEDYEGGGCRFLR---YNCSVRAPRKGWALMHP-GRLTHYHE 487
Cdd:smart00702  74 DAQVARYGPG--GHYGPHVDNFlygdrIATFILYLN---DVEEGGELVFPGlrlMVVATVKPKKGDLLFFPsGHGRSLHG 148

                          170
                   ....*....|....*.
gi 1958774364  488 GLPTTKGTRYIAVSFV 503
Cdd:smart00702 149 VCPVTRGSRWAITGWI 164
GT_LH1 cd23004
catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 1 (LH1) and similar ...
 1-32 5.37e-16

catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 1 (LH1) and similar proteins; LH1 (EC 1.14.11.4), also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1), forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines may serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links. LH1 is part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linkling of collagen fibrils. This model corresponds to the N-terminal conserved domain of LH1, which shows high sequence similarity with catalytic glycosyltransferase (GT) domain of LH3.


Pssm-ID: 438560  Cd Length: 230  Bit Score: 77.15  E-value: 5.37e-16
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1958774364   1 MGHVRARNLAYDTLPVVIHGNGPTKLQVNYLG 32
Cdd:cd23004   199 DGRVRARNLLYDTLPVIIHGNGPTKLQLNYLG 230
2OG-FeII_Oxy pfam03171
2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and ...
 415-505 5.22e-10

2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.


Pssm-ID: 397334 [Multi-domain]  Cd Length: 101  Bit Score: 56.31  E-value: 5.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958774364 415 FDLAFVVRY-KPDEQPSLM----PHHDASTFTINIALNRVGEDYEGGGCrFLRYNCSVRA--PRKG--WALMHPGRL-TH 484
Cdd:pfam03171   1 PDQCLVLNYyPPHPDPDLTlglgPHTDASILTILLQDDVGGLQVFKDGK-WIDVPPLPGAlvVNIGdqLELLSNGRYkSV 79

                          90       100
                  ....*....|....*....|..
gi 1958774364 485 YHEGLPTTKG-TRYIAVSFVDP 505
Cdd:pfam03171  80 LHRVLPVNKGkERISIAFFLRP 101
 
Name Accession Description Interval E-value
P4Hc smart00702
Prolyl 4-hydroxylase alpha subunit homologues; Mammalian enzymes catalyse hydroxylation of ...
 340-503 1.79e-25

Prolyl 4-hydroxylase alpha subunit homologues; Mammalian enzymes catalyse hydroxylation of collagen, for example. Prokaryotic enzymes might catalyse hydroxylation of antibiotic peptides. These are 2-oxoglutarate-dependent dioxygenases, requiring 2-oxoglutarate and dioxygen as cosubstrates and ferrous iron as a cofactor.


Pssm-ID: 214780  Cd Length: 165  Bit Score: 102.47  E-value: 1.79e-25
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958774364  340 TEVACDELVEEMEHYGqWSLGDNKDNRIQGgyenvPTIDIHMNQITFeREWHK--FLVEYIAPLTEKLYPGYY-TKAQFD 416
Cdd:smart00702   1 SPAECQKLLEEAEPLG-WRGEVTRGIGNPN-----ETSQYRQSNGTW-LELLErdLVIERIRQRLADFLGLLAgLPLSAE 73

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958774364  417 LAFVVRYKPDeqPSLMPHHDAS-----TFTINIALNrvgEDYEGGGCRFLR---YNCSVRAPRKGWALMHP-GRLTHYHE 487
Cdd:smart00702  74 DAQVARYGPG--GHYGPHVDNFlygdrIATFILYLN---DVEEGGELVFPGlrlMVVATVKPKKGDLLFFPsGHGRSLHG 148

                          170
                   ....*....|....*.
gi 1958774364  488 GLPTTKGTRYIAVSFV 503
Cdd:smart00702 149 VCPVTRGSRWAITGWI 164
GT_LH1 cd23004
catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 1 (LH1) and similar ...
 1-32 5.37e-16

catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 1 (LH1) and similar proteins; LH1 (EC 1.14.11.4), also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 (PLOD1), forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines may serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links. LH1 is part of a complex composed of PLOD1, P3H3 and P3H4 that catalyzes hydroxylation of lysine residues in collagen alpha chains and is required for normal assembly and cross-linkling of collagen fibrils. This model corresponds to the N-terminal conserved domain of LH1, which shows high sequence similarity with catalytic glycosyltransferase (GT) domain of LH3.


Pssm-ID: 438560  Cd Length: 230  Bit Score: 77.15  E-value: 5.37e-16
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1958774364   1 MGHVRARNLAYDTLPVVIHGNGPTKLQVNYLG 32
Cdd:cd23004   199 DGRVRARNLLYDTLPVIIHGNGPTKLQLNYLG 230
GT_LH3 cd23002
catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 3 (LH3) and similar ...
 4-32 1.75e-11

catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 3 (LH3) and similar proteins; Lysyl hydroxylase 3 (LH3; EC 1.14.11.4/EC 2.4.1.50/EC 2.4.1.66), also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 (PLOD3), or multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3, is a multifunctional enzyme that catalyzes a series of essential post-translational modifications on Lys residues in procollagen. It converts collagen lysines into 1,2-glucosylgalactosyl-5-hydroxylysines through three consecutive reactions: hydroxylation of collagen lysines (LH activity), N-linked conjugation of galactose to hydroxylysines (GT activity), and conjugation of glucose to galactosyl-5-hydroxylysines (GGT activity). LH3 monomer encompasses three domains; the first two N-terminal domains (catalytic glycosyltransferase domain and accessory domain) show Rossmann-fold architectures reminiscent of glycosyltransferases, whereas the C-terminal domain is characterized by a double-stranded beta-helix (DSBH) fold, highly conserved among the 2-oxoglutarate, Fe2+-dependent dioxygenases. This model corresponds to the N-terminal catalytic glycosyltransferase (GT) domain, which is solely responsible for glycosyltransferase activities (both GT and GGT).


Pssm-ID: 438558  Cd Length: 230  Bit Score: 64.06  E-value: 1.75e-11
                          10        20
                  ....*....|....*....|....*....
gi 1958774364   4 VRARNLAYDTLPVVIHGNGPTKLQVNYLG 32
Cdd:cd23002   202 VRIRNVAYDTLPIVVHGNGPTKLQLNYLG 230
GT_LH2 cd23003
catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 2 (LH2) and similar ...
 2-32 4.87e-10

catalytic glycosyltransferase (GT) domain found in lysyl hydroxylase 2 (LH2) and similar proteins; Lysyl hydroxylase 2 (LH2; EC 1.14.11.4), also called procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 (PLOD2), forms hydroxylysine residues in -Xaa-Lys-Gly- sequences in collagens. These hydroxylysines serve as sites of attachment for carbohydrate units and are essential for the stability of the intermolecular collagen cross-links. The model corresponds to the N-terminal conserved domain of LH2, which shows high sequence similarity with catalytic glycosyltransferase (GT) domain of LH3.


Pssm-ID: 438559  Cd Length: 230  Bit Score: 59.84  E-value: 4.87e-10
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1958774364   2 GHVRARNLAYDTLPVVIHGNGPTKLQVNYLG 32
Cdd:cd23003   200 GKARVRNTVYETLPVVIHGNGPTKLLLNYLG 230
2OG-FeII_Oxy pfam03171
2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and ...
 415-505 5.22e-10

2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily. This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity EC:1.14.11.2 catalysing the reaction: Procollagen L-proline + 2-oxoglutarate + O2 <=> procollagen trans- 4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site. The family also includes lysyl hydrolases, isopenicillin synthases and AlkB.


Pssm-ID: 397334 [Multi-domain]  Cd Length: 101  Bit Score: 56.31  E-value: 5.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958774364 415 FDLAFVVRY-KPDEQPSLM----PHHDASTFTINIALNRVGEDYEGGGCrFLRYNCSVRA--PRKG--WALMHPGRL-TH 484
Cdd:pfam03171   1 PDQCLVLNYyPPHPDPDLTlglgPHTDASILTILLQDDVGGLQVFKDGK-WIDVPPLPGAlvVNIGdqLELLSNGRYkSV 79

                          90       100
                  ....*....|....*....|..
gi 1958774364 485 YHEGLPTTKG-TRYIAVSFVDP 505
Cdd:pfam03171  80 LHRVLPVNKGkERISIAFFLRP 101
2OG-FeII_Oxy_3 pfam13640
2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and ...
 418-503 3.43e-04

2OG-Fe(II) oxygenase superfamily; This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.


Pssm-ID: 463943  Cd Length: 94  Bit Score: 39.67  E-value: 3.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958774364 418 AFVVRYKPDEQpsLMPHHDAST---------FTINIALNRvGEDYEGGGCRFL-RYNCSVRAPRKGWALMHPGRLTHYHE 487
Cdd:pfam13640   1 LQLARYGDGGF--YKPHLDFFEgaegggqrrLTVVLYLND-WEEEEGGELVLYdGDGVEDIKPKKGRLVLFPSSELSLHE 77

                          90
                  ....*....|....*.
gi 1958774364 488 GLPTTKGTRYIAVSFV 503
Cdd:pfam13640  78 VLPVTGGERWSITGWF 93
 
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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