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Conserved domains on  [gi|19114718|ref|NP_593806|]
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histone demethylase Jmj1 [Schizosaccharomyces pombe]

Protein Classification

bifunctional arginine demethylase and lysyl-hydroxylase( domain architecture ID 10492996)

bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 is a dioxygenase that can both act as a arginine demethylase and a lysyl-hydroxylase

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 225-332 4.31e-23

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.


:

Pssm-ID: 396791  Cd Length: 114  Bit Score: 93.90  E-value: 4.31e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114718   225 FAYLGSHLTTTGLHTDVYASHS-FSVNLCGVKCWLFIDPKDLQTIASLYDDQ-------QLPSWITKDDLFRgpLVNHRH 296
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSiNYLHFGAPKVWYIIPPEYAEKFEKVLSDHfggeqpdDLLHLNTIISPKQ--LRENGI 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 19114718   297 LIKILFQYPGQTVFVPSGWYHQVLNIGTTLSINHNW 332
Cdd:pfam02373  79 PVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 225-332 4.31e-23

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 93.90  E-value: 4.31e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114718   225 FAYLGSHLTTTGLHTDVYASHS-FSVNLCGVKCWLFIDPKDLQTIASLYDDQ-------QLPSWITKDDLFRgpLVNHRH 296
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSiNYLHFGAPKVWYIIPPEYAEKFEKVLSDHfggeqpdDLLHLNTIISPKQ--LRENGI 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 19114718   297 LIKILFQYPGQTVFVPSGWYHQVLNIGTTLSINHNW 332
Cdd:pfam02373  79 PVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
cupin_OxDC-like cd20306
Oxalate decarboxylase (OxDC)-like cupin domain; This subfamily contains bacterial and ...
 305-323 8.95e-03

Oxalate decarboxylase (OxDC)-like cupin domain; This subfamily contains bacterial and eukaryotic cupin domains of proteins homologous to oxalate decarboxylase (OxDC; EC 4.1.1.2) such as MSMEG_2254, a putative OxDC from Mycobacterium smegmatis. OxDC is a manganese-dependent bicupin that catalyzes the conversion of oxalate to formate and carbon dioxide, utilizing dioxygen as a cofactor. It is evolutionarily related to oxalate oxidase (OxOx or germin; EC 1.2.3.4) which, in contrast, converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. OxDC is classified as a bicupin because it contains two cupin folds with each domain containing one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues.


Pssm-ID: 380440 [Multi-domain]  Cd Length: 151  Bit Score: 36.80  E-value: 8.95e-03
                        10
                ....*....|....*....
gi 19114718 305 PGQTVFVPSGWYHQVLNIG 323
Cdd:cd20306  84 PGQVVFIPQGWLHWIENVG 102
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 225-332 4.31e-23

JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain proteins may be protein hydroxylases that catalyze a novel histone modification. This is confirmed to be a hydroxylase: the human JmjC protein named Tyw5p unexpectedly acts in the biosynthesis of a hypermodified nucleoside, hydroxy-wybutosine, in tRNA-Phe by catalysing hydroxylation.


Pssm-ID: 396791  Cd Length: 114  Bit Score: 93.90  E-value: 4.31e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114718   225 FAYLGSHLTTTGLHTDVYASHS-FSVNLCGVKCWLFIDPKDLQTIASLYDDQ-------QLPSWITKDDLFRgpLVNHRH 296
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSiNYLHFGAPKVWYIIPPEYAEKFEKVLSDHfggeqpdDLLHLNTIISPKQ--LRENGI 78

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 19114718   297 LIKILFQYPGQTVFVPSGWYHQVLNIGTTLSINHNW 332
Cdd:pfam02373  79 PVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
Cupin_8 pfam13621
Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
 118-332 5.15e-04

Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.


Pssm-ID: 463936  Cd Length: 251  Bit Score: 41.59  E-value: 5.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114718   118 SPNYEYLEENYGTIPVPLA----------YCNEKDRYGSQRRETVPLKSALHELRDE-------QVQLQCrqAPSNQALK 180
Cdd:pfam13621  33 SSLLDYLKDKYGDVEVTVEvtpdgradrlFYNDDFTFVNPKEERMPFGEFLDRLEAGedtdtapYAYLQS--DNLRSEFP 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114718   181 SLYAKDmhlfrhldpaDFPystpdiFADDwlnayVIDCESDDFRFaYLGSHLTTTGLHTDVYasHSFSVNLCGVKCWLFI 260
Cdd:pfam13621 111 ELLEDN----------DLP------FATE-----AFGGEPDAVNL-WMGNGRSVTSLHYDHY--ENLYCVVRGRKRFTLF 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19114718   261 DPKDLQT--IASLYDDQQLPSWITKD----DLFRGPL---VNHRHLIKIlfqYPGQTVFVPSGWYHQV--LNiGTTLSIN 329
Cdd:pfam13621 167 PPSDVPNlyPGPLEPTPEGQVFSLVDplapDFERFPRfrdAARPLVVTL---NPGDVLYLPALWWHHVesLD-PFNIAVN 242


                  ...
gi 19114718   330 HNW 332
Cdd:pfam13621 243 YWY 245
cupin_OxDC-like cd20306
Oxalate decarboxylase (OxDC)-like cupin domain; This subfamily contains bacterial and ...
 305-323 8.95e-03

Oxalate decarboxylase (OxDC)-like cupin domain; This subfamily contains bacterial and eukaryotic cupin domains of proteins homologous to oxalate decarboxylase (OxDC; EC 4.1.1.2) such as MSMEG_2254, a putative OxDC from Mycobacterium smegmatis. OxDC is a manganese-dependent bicupin that catalyzes the conversion of oxalate to formate and carbon dioxide, utilizing dioxygen as a cofactor. It is evolutionarily related to oxalate oxidase (OxOx or germin; EC 1.2.3.4) which, in contrast, converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. OxDC is classified as a bicupin because it contains two cupin folds with each domain containing one manganese binding site, with four manganese binding residues (three histidines and one glutamate) conserved as well as a number of hydrophobic residues.


Pssm-ID: 380440 [Multi-domain]  Cd Length: 151  Bit Score: 36.80  E-value: 8.95e-03
                        10
                ....*....|....*....
gi 19114718 305 PGQTVFVPSGWYHQVLNIG 323
Cdd:cd20306  84 PGQVVFIPQGWLHWIENVG 102
 
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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