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Conserved domains on  [gi|386767355|ref|NP_001246194|]
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lysine demethylase 4A, isoform B [Drosophila melanogaster]

Protein Classification

lysine-specific demethylase( domain architecture ID 10338135)

lysine-specific demethylase is a jumonji C domain-containing (JMJD) family histone demethylase demethylates specific residues of histone, similar to Drosophila melanogaster lysine-specific demethylase 4A that specifically demethylates 'Lys-9' and 'Lys-36' residues 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:0032452|GO:0006355
PubMed:  25372754|37832177|35558079|19478949|14697267
SCOP:  3001825

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 ...
 182-298 5.70e-55

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: 179.42  E-value: 5.70e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386767355  182 YLYFGMWKSSFAWHTEDMDLYSINYLHFGAPKTWYAIPPAYGRRLEKLANETFSenyQECNAYLRHKMTMISPKVLRQHN 261
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFG---GEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 386767355  262 IPYNKITQEAGEIMITFPFGYHAGFNHGFNGAESTNF 298
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjN super family cl15840
jmjN domain;
17-59 6.56e-12

jmjN domain;


The actual alignment was detected with superfamily member smart00545:

Pssm-ID: 472837  Cd Length: 42  Bit Score: 59.97  E-value: 6.56e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 386767355    17 RIMTFRPSYEEFQNFSAYIEYIESRgAHLAGLAKIQPPAEWVP 59
Cdd:smart00545   1 EIPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 182-298 5.70e-55

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: 179.42  E-value: 5.70e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386767355  182 YLYFGMWKSSFAWHTEDMDLYSINYLHFGAPKTWYAIPPAYGRRLEKLANETFSenyQECNAYLRHKMTMISPKVLRQHN 261
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFG---GEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 386767355  262 IPYNKITQEAGEIMITFPFGYHAGFNHGFNGAESTNF 298
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 155-212 4.92e-14

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: 66.51  E-value: 4.92e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 386767355   155 WNIGRLDTILNLVNtDYNIIIDGVNTA-YLYFGMWKSSFAWHTEDMDLysINYLHFGAP 212
Cdd:smart00558   3 WNLAKLPFKLNLLS-DLPEDIPGPDVGpYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 17-59 6.56e-12

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


Pssm-ID: 128818  Cd Length: 42  Bit Score: 59.97  E-value: 6.56e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 386767355    17 RIMTFRPSYEEFQNFSAYIEYIESRgAHLAGLAKIQPPAEWVP 59
Cdd:smart00545   1 EIPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
JmjN pfam02375
jmjN domain;
19-53 4.86e-10

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 54.60  E-value: 4.86e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 386767355   19 MTFRPSYEEFQNFSAYIEYIESRGAHlAGLAKIQP 53
Cdd:pfam02375   1 PVFYPTEEEFKDPLKYIEKIRPLGEK-YGICKIVP 34
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
 182-298 5.70e-55

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: 179.42  E-value: 5.70e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 386767355  182 YLYFGMWKSSFAWHTEDMDLYSINYLHFGAPKTWYAIPPAYGRRLEKLANETFSenyQECNAYLRHKMTMISPKVLRQHN 261
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSINYLHFGAPKVWYIIPPEYAEKFEKVLSDHFG---GEQPDDLLHLNTIISPKQLRENG 77

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 386767355  262 IPYNKITQEAGEIMITFPFGYHAGFNHGFNGAESTNF 298
Cdd:pfam02373  78 IPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
 155-212 4.92e-14

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: 66.51  E-value: 4.92e-14
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 386767355   155 WNIGRLDTILNLVNtDYNIIIDGVNTA-YLYFGMWKSSFAWHTEDMDLysINYLHFGAP 212
Cdd:smart00558   3 WNLAKLPFKLNLLS-DLPEDIPGPDVGpYLYMGMAGSTTPWHIDDYDL--VNYLHQGAG 58
JmjN smart00545
Small domain found in the jumonji family of transcription factors; To date, this domain always ...
 17-59 6.56e-12

Small domain found in the jumonji family of transcription factors; To date, this domain always co-occurs with the JmjC domain (although the reverse is not true).


Pssm-ID: 128818  Cd Length: 42  Bit Score: 59.97  E-value: 6.56e-12
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 386767355    17 RIMTFRPSYEEFQNFSAYIEYIESRgAHLAGLAKIQPPAEWVP 59
Cdd:smart00545   1 EIPVFYPTMEEFKDPLAYISKIRPQ-AEKYGICKVVPPKSWKP 42
JmjN pfam02375
jmjN domain;
19-53 4.86e-10

jmjN domain;


Pssm-ID: 460542  Cd Length: 34  Bit Score: 54.60  E-value: 4.86e-10
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 386767355   19 MTFRPSYEEFQNFSAYIEYIESRGAHlAGLAKIQP 53
Cdd:pfam02375   1 PVFYPTEEEFKDPLKYIEKIRPLGEK-YGICKIVP 34
 
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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