NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1884086674|ref|NP_075383|]
View 

2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform 1 [Homo sapiens]

Protein Classification

cupin domain-containing protein( domain architecture ID 1562428)

cupin domain-containing protein, part of a functionally diverse superfamily with the active site generally located at the center of a conserved domain forming a beta-barrel fold

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 ...
176-284 1.73e-19

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: 83.50  E-value: 1.73e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674 176 FVYAGPAGSWSPFHADIFRSFS-WSVNVCGRKKWLLFPPGQ----EEALRDR-HGNLPYDVTSPAlcdTHLHPRNQLAG- 248
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSiNYLHFGAPKVWYIIPPEYaekfEKVLSDHfGGEQPDDLLHLN---TIISPKQLRENg 77
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1884086674 249 -PPLEITQEAGEMVFVPSGWHHQVHNLDDTISINHNW 284
Cdd:pfam02373  78 iPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
Cupin_8 super family cl46322
Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
42-284 5.06e-17

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


The actual alignment was detected with superfamily member pfam13621:

Pssm-ID: 463936  Cd Length: 251  Bit Score: 80.11  E-value: 5.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674  42 ADFVRGFLLPNLPCVFSSAfTQGWGSRRRWVTPAGRpdfDHLLRTYGDVVVPVA-----NCGVQEYNS-----NPKEH-M 110
Cdd:pfam13621   2 AEFFREYVAKNKPVVIRGA-VKDWPAVQKWTDSSLL---DYLKDKYGDVEVTVEvtpdgRADRLFYNDdftfvNPKEErM 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674 111 TLRDYItywkEYIQAGYSSPRGC-LYLKDWHLCRDFP-VEDVFTLPvyFSSDWLNEFWDALDVddyrfvYAGPAGSWSPF 188
Cdd:pfam13621  78 PFGEFL----DRLEAGEDTDTAPyAYLQSDNLRSEFPeLLEDNDLP--FATEAFGGEPDAVNL------WMGNGRSVTSL 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674 189 HADIFRSfsWSVNVCGRKKWLLFPPGQEEALRDRHGNLPYDVTSPALCDTH-----LHPRNQLAGPPLEITQEAGEMVFV 263
Cdd:pfam13621 146 HYDHYEN--LYCVVRGRKRFTLFPPSDVPNLYPGPLEPTPEGQVFSLVDPLapdfeRFPRFRDAARPLVVTLNPGDVLYL 223
                         250       260
                  ....*....|....*....|..
gi 1884086674 264 PSGWHHQVHNLDD-TISINHNW 284
Cdd:pfam13621 224 PALWWHHVESLDPfNIAVNYWY 245
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
176-284 1.73e-19

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: 83.50  E-value: 1.73e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674 176 FVYAGPAGSWSPFHADIFRSFS-WSVNVCGRKKWLLFPPGQ----EEALRDR-HGNLPYDVTSPAlcdTHLHPRNQLAG- 248
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSiNYLHFGAPKVWYIIPPEYaekfEKVLSDHfGGEQPDDLLHLN---TIISPKQLRENg 77
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1884086674 249 -PPLEITQEAGEMVFVPSGWHHQVHNLDDTISINHNW 284
Cdd:pfam02373  78 iPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
Cupin_8 pfam13621
Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
42-284 5.06e-17

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


Pssm-ID: 463936  Cd Length: 251  Bit Score: 80.11  E-value: 5.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674  42 ADFVRGFLLPNLPCVFSSAfTQGWGSRRRWVTPAGRpdfDHLLRTYGDVVVPVA-----NCGVQEYNS-----NPKEH-M 110
Cdd:pfam13621   2 AEFFREYVAKNKPVVIRGA-VKDWPAVQKWTDSSLL---DYLKDKYGDVEVTVEvtpdgRADRLFYNDdftfvNPKEErM 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674 111 TLRDYItywkEYIQAGYSSPRGC-LYLKDWHLCRDFP-VEDVFTLPvyFSSDWLNEFWDALDVddyrfvYAGPAGSWSPF 188
Cdd:pfam13621  78 PFGEFL----DRLEAGEDTDTAPyAYLQSDNLRSEFPeLLEDNDLP--FATEAFGGEPDAVNL------WMGNGRSVTSL 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674 189 HADIFRSfsWSVNVCGRKKWLLFPPGQEEALRDRHGNLPYDVTSPALCDTH-----LHPRNQLAGPPLEITQEAGEMVFV 263
Cdd:pfam13621 146 HYDHYEN--LYCVVRGRKRFTLFPPSDVPNLYPGPLEPTPEGQVFSLVDPLapdfeRFPRFRDAARPLVVTLNPGDVLYL 223
                         250       260
                  ....*....|....*....|..
gi 1884086674 264 PSGWHHQVHNLDD-TISINHNW 284
Cdd:pfam13621 224 PALWWHHVESLDPfNIAVNYWY 245
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
157-198 3.08e-03

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: 35.69  E-value: 3.08e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1884086674  157 FSSDWLNEFWDALD-VDDYRFVYAGPAGSWSPFHADIFRSFSW 198
Cdd:smart00558  10 FKLNLLSDLPEDIPgPDVGPYLYMGMAGSTTPWHIDDYDLVNY 52
 
Name Accession Description Interval E-value
JmjC pfam02373
JmjC domain, hydroxylase; The JmjC domain belongs to the Cupin superfamily. JmjC-domain ...
176-284 1.73e-19

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: 83.50  E-value: 1.73e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674 176 FVYAGPAGSWSPFHADIFRSFS-WSVNVCGRKKWLLFPPGQ----EEALRDR-HGNLPYDVTSPAlcdTHLHPRNQLAG- 248
Cdd:pfam02373   1 WLYLGMPFSTTPWHIEDQGLYSiNYLHFGAPKVWYIIPPEYaekfEKVLSDHfGGEQPDDLLHLN---TIISPKQLRENg 77
                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 1884086674 249 -PPLEITQEAGEMVFVPSGWHHQVHNLDDTISINHNW 284
Cdd:pfam02373  78 iPVYRFVQKPGEFVFTFPGWYHQVFNLGFNIAEAVNF 114
Cupin_8 pfam13621
Cupin-like domain; This cupin like domain shares similarity to the JmjC domain.
42-284 5.06e-17

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


Pssm-ID: 463936  Cd Length: 251  Bit Score: 80.11  E-value: 5.06e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674  42 ADFVRGFLLPNLPCVFSSAfTQGWGSRRRWVTPAGRpdfDHLLRTYGDVVVPVA-----NCGVQEYNS-----NPKEH-M 110
Cdd:pfam13621   2 AEFFREYVAKNKPVVIRGA-VKDWPAVQKWTDSSLL---DYLKDKYGDVEVTVEvtpdgRADRLFYNDdftfvNPKEErM 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674 111 TLRDYItywkEYIQAGYSSPRGC-LYLKDWHLCRDFP-VEDVFTLPvyFSSDWLNEFWDALDVddyrfvYAGPAGSWSPF 188
Cdd:pfam13621  78 PFGEFL----DRLEAGEDTDTAPyAYLQSDNLRSEFPeLLEDNDLP--FATEAFGGEPDAVNL------WMGNGRSVTSL 145
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1884086674 189 HADIFRSfsWSVNVCGRKKWLLFPPGQEEALRDRHGNLPYDVTSPALCDTH-----LHPRNQLAGPPLEITQEAGEMVFV 263
Cdd:pfam13621 146 HYDHYEN--LYCVVRGRKRFTLFPPSDVPNLYPGPLEPTPEGQVFSLVDPLapdfeRFPRFRDAARPLVVTLNPGDVLYL 223
                         250       260
                  ....*....|....*....|..
gi 1884086674 264 PSGWHHQVHNLDD-TISINHNW 284
Cdd:pfam13621 224 PALWWHHVESLDPfNIAVNYWY 245
JmjC smart00558
A domain family that is part of the cupin metalloenzyme superfamily; Probable enzymes, but of ...
157-198 3.08e-03

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: 35.69  E-value: 3.08e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1884086674  157 FSSDWLNEFWDALD-VDDYRFVYAGPAGSWSPFHADIFRSFSW 198
Cdd:smart00558  10 FKLNLLSDLPEDIPgPDVGPYLYMGMAGSTTPWHIDDYDLVNY 52
 
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