NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|955388632|ref|XP_014627316|]
View 

lysine-specific demethylase JMJ25 isoform X2 [Glycine max]

Protein Classification

lysine-specific demethylase( domain architecture ID 15468173)

lysine-specific demethylase is a jumonji C domain-containing (JMJD) family histone demethylase demethylates specific residues of histone, similar to human lysine-specific demethylases 3A and 3B that specifically demethylate 'Lys-9' of histone H3, thereby playing a central role in the histone code

CATH:  2.60.120.10
EC:  1.14.11.-
Gene Ontology:  GO:0046872|GO:0141052|GO:0006355
PubMed:  25372754|37832177|35558079|19478949|14697267
SCOP:  3001825

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
cupin_RmlC-like super family cl40423
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 749-845 8.73e-16

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


The actual alignment was detected with superfamily member pfam02373:

Pssm-ID: 477354  Cd Length: 114  Bit Score: 74.26  E-value: 8.73e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955388632  749 ALWDIFRRQDVPKLQEYLKKHFREFRhvhccpLKQVIH--PIHDQTFYLTMEHKRKLKEEyGIEPWTFIQKLGDAVFIPV 826
Cdd:pfam02373  23 INYLHFGAPKVWYIIPPEYAEKFEKV------LSDHFGgeQPDDLLHLNTIISPKQLREN-GIPVYRFVQKPGEFVFTFP 95

                          90
                  ....*....|....*....
gi 955388632  827 GCPHQVRNLKSCIKVAMDF 845
Cdd:pfam02373  96 GWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 555-628 1.01e-07

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


:

Pssm-ID: 214721  Cd Length: 58  Bit Score: 49.17  E-value: 1.01e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 955388632   555 CAEFISSLPFKeytdphkgsLNLAVKLPNGSLKPDLGPktYIAYGFPqelgrgDSVTKLHCDMSDAVNVLTHIA 628
Cdd:smart00558   1 QLWNLAKLPFK---------LNLLSDLPEDIPGPDVGP--YLYMGMA------GSTTPWHIDDYDLVNYLHQGA 57
zf-4CXXC_R1 super family cl20401
Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor ...
 132-189 1.14e-06

Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type.


The actual alignment was detected with superfamily member pfam10497:

Pssm-ID: 463117  Cd Length: 99  Bit Score: 47.64  E-value: 1.14e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 955388632  132 TCHQC--KRNDKGRVVRCKCCNKRR--FCLLCLQAWYPHLKENDIAEK---CPVCRGNCNCKACL 189
Cdd:pfam10497   8 TCHQCrqKTLDTKTSCRNSQCKGVRgqFCGDCLRNRYGENVEEALANPdwiCPKCRGICNCSFCR 72
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 749-845 8.73e-16

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: 74.26  E-value: 8.73e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955388632  749 ALWDIFRRQDVPKLQEYLKKHFREFRhvhccpLKQVIH--PIHDQTFYLTMEHKRKLKEEyGIEPWTFIQKLGDAVFIPV 826
Cdd:pfam02373  23 INYLHFGAPKVWYIIPPEYAEKFEKV------LSDHFGgeQPDDLLHLNTIISPKQLREN-GIPVYRFVQKPGEFVFTFP 95

                          90
                  ....*....|....*....
gi 955388632  827 GCPHQVRNLKSCIKVAMDF 845
Cdd:pfam02373  96 GWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 555-628 1.01e-07

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 49.17  E-value: 1.01e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 955388632   555 CAEFISSLPFKeytdphkgsLNLAVKLPNGSLKPDLGPktYIAYGFPqelgrgDSVTKLHCDMSDAVNVLTHIA 628
Cdd:smart00558   1 QLWNLAKLPFK---------LNLLSDLPEDIPGPDVGP--YLYMGMA------GSTTPWHIDDYDLVNYLHQGA 57
zf-4CXXC_R1 pfam10497
Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor ...
 132-189 1.14e-06

Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type.


Pssm-ID: 463117  Cd Length: 99  Bit Score: 47.64  E-value: 1.14e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 955388632  132 TCHQC--KRNDKGRVVRCKCCNKRR--FCLLCLQAWYPHLKENDIAEK---CPVCRGNCNCKACL 189
Cdd:pfam10497   8 TCHQCrqKTLDTKTSCRNSQCKGVRgqFCGDCLRNRYGENVEEALANPdwiCPKCRGICNCSFCR 72
RING-HC_RNF219 cd16562
RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; ...
 130-180 1.28e-03

RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; RNF219 may function as a modulator of late-onset Alzheimer's disease (LOAD) associated amyloid beta A4 precursor protein (APP) endocytosis and metabolism. It genetically interacts with apolipoprotein E epsilon4 allele (APOE4). Thus, a genetic variant of RNF219 was found to affect amyloid deposition in human brain and LOAD age-of-onset. Moreover, common genetic variants at the RNF219 locus had been associated with alternations in lipid metabolism, cognitive performance and central nervous system ventricle volume. RNF219 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438224 [Multi-domain]  Cd Length: 45  Bit Score: 37.42  E-value: 1.28e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 955388632 130 PLTCHQCKRNDKGRVVrckCCNKRRFCLLCLQAWyphLKENDIaekCPVCR 180
Cdd:cd16562    1 PISCHICLGKVRQPVI---CSNNHVFCSSCMDVW---LKNNNQ---CPACR 42
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 749-845 8.73e-16

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: 74.26  E-value: 8.73e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 955388632  749 ALWDIFRRQDVPKLQEYLKKHFREFRhvhccpLKQVIH--PIHDQTFYLTMEHKRKLKEEyGIEPWTFIQKLGDAVFIPV 826
Cdd:pfam02373  23 INYLHFGAPKVWYIIPPEYAEKFEKV------LSDHFGgeQPDDLLHLNTIISPKQLREN-GIPVYRFVQKPGEFVFTFP 95

                          90
                  ....*....|....*....
gi 955388632  827 GCPHQVRNLKSCIKVAMDF 845
Cdd:pfam02373  96 GWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 555-628 1.01e-07

A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of unknown functions, that regulate chromatin reorganisation processes (Clissold and Ponting, in press).


Pssm-ID: 214721  Cd Length: 58  Bit Score: 49.17  E-value: 1.01e-07
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 955388632   555 CAEFISSLPFKeytdphkgsLNLAVKLPNGSLKPDLGPktYIAYGFPqelgrgDSVTKLHCDMSDAVNVLTHIA 628
Cdd:smart00558   1 QLWNLAKLPFK---------LNLLSDLPEDIPGPDVGP--YLYMGMA------GSTTPWHIDDYDLVNYLHQGA 57
zf-4CXXC_R1 pfam10497
Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor ...
 132-189 1.14e-06

Zinc-finger domain of monoamine-oxidase A repressor R1; R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type.


Pssm-ID: 463117  Cd Length: 99  Bit Score: 47.64  E-value: 1.14e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 955388632  132 TCHQC--KRNDKGRVVRCKCCNKRR--FCLLCLQAWYPHLKENDIAEK---CPVCRGNCNCKACL 189
Cdd:pfam10497   8 TCHQCrqKTLDTKTSCRNSQCKGVRgqFCGDCLRNRYGENVEEALANPdwiCPKCRGICNCSFCR 72
RING-HC_RNF219 cd16562
RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; ...
 130-180 1.28e-03

RING finger, HC subclass, found in RING finger protein 219 (RNF219) and similar proteins; RNF219 may function as a modulator of late-onset Alzheimer's disease (LOAD) associated amyloid beta A4 precursor protein (APP) endocytosis and metabolism. It genetically interacts with apolipoprotein E epsilon4 allele (APOE4). Thus, a genetic variant of RNF219 was found to affect amyloid deposition in human brain and LOAD age-of-onset. Moreover, common genetic variants at the RNF219 locus had been associated with alternations in lipid metabolism, cognitive performance and central nervous system ventricle volume. RNF219 contains a C3HC4-type RING-HC finger.


Pssm-ID: 438224 [Multi-domain]  Cd Length: 45  Bit Score: 37.42  E-value: 1.28e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 955388632 130 PLTCHQCKRNDKGRVVrckCCNKRRFCLLCLQAWyphLKENDIaekCPVCR 180
Cdd:cd16562    1 PISCHICLGKVRQPVI---CSNNHVFCSSCMDVW---LKNNNQ---CPACR 42
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH