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Protein

Putative oxidoreductase GLYR1

Gene

GLYR1

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Putative oxidoreductase that is recruited on chromatin and promotes KDM1B demethylase activity (PubMed:23260659). Recognizes and binds trimethylated 'Lys-36' of histone H3 (H3K36me3) (PubMed:20850016). Regulates p38 MAP kinase activity by mediating stress activation of p38alpha/MAPK14 and specifically regulating MAPK14 signaling (PubMed:16352664). Indirectly promotes phosphorylation of MAPK14 and activation of ATF2 (PubMed:16352664). The phosphorylation of MAPK14 requires upstream activity of MAP2K4 and MAP2K6 (PubMed:16352664).3 Publications

Miscellaneous

The conserved NAD-binding sites and sequence similarity to plant dehydrogenases suggest that this protein may have oxidoreductase activity.Curated

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei217Required to promote KDM1B demethylase activity toward histone H3K4me1 and H3K4me21 Publication1
Binding sitei362NADCombined sources1 Publication1
Binding sitei505NADCombined sources1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi168 – 180A.T hookCuratedAdd BLAST13
Nucleotide bindingi271 – 285NADCombined sources1 PublicationAdd BLAST15

GO - Molecular functioni

Keywordsi

Molecular functionDNA-binding, Oxidoreductase
LigandNAD

Names & Taxonomyi

Protein namesi
Recommended name:
Putative oxidoreductase GLYR1 (EC:1.-.-.-)
Alternative name(s):
3-hydroxyisobutyrate dehydrogenase-like protein
Cytokine-like nuclear factor N-PAC
Glyoxylate reductase 1 homolog
Nuclear protein NP60
Nuclear protein of 60 kDa
Gene namesi
Name:GLYR1
Synonyms:HIBDL, NP60
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 16

Organism-specific databases

EuPathDBiHostDB:ENSG00000140632.16
HGNCiHGNC:24434 GLYR1
MIMi610660 gene
neXtProtiNX_Q49A26

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi214D → A: Slightly reduced stimulation of KDM1B demethylase activity, but normal KDM1B-binding. 1 Publication1
Mutagenesisi216H → A: Slightly reduced stimulation of KDM1B demethylase activity, but normal KDM1B-binding. 1 Publication1
Mutagenesisi217F → A: Abolished stimulation of KDM1B demethylase activity, reduced affinity for histone H3 of the dimer with KDM1B, but normal KDM1B-binding. 1 Publication1
Mutagenesisi219H → A: Impaired KDM1B-binding and abolished stimulation of KDM1B demethylase activity; when associated with A-223. 1 Publication1
Mutagenesisi220 – 222FLL → AAA: Impaired KDM1B-binding and abolished stimulation of KDM1B demethylase activity. 1 Publication3
Mutagenesisi223S → A: Impaired KDM1B-binding and abolished stimulation of KDM1B demethylase activity; when associated with A-219. 1 Publication1

Organism-specific databases

DisGeNETi84656
OpenTargetsiENSG00000140632
PharmGKBiPA165450093

Polymorphism and mutation databases

BioMutaiGLYR1
DMDMi269849681

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003121211 – 553Putative oxidoreductase GLYR1Add BLAST553

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei130PhosphoserineCombined sources1
Cross-linki135Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei167PhosphoserineCombined sources1
Cross-linki176Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki179Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki201Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki211Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki227Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki237Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki240Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki269Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Cross-linki302Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)Combined sources
Modified residuei540PhosphoserineCombined sources1

Keywords - PTMi

Isopeptide bond, Phosphoprotein, Ubl conjugation

Proteomic databases

EPDiQ49A26
MaxQBiQ49A26
PaxDbiQ49A26
PeptideAtlasiQ49A26
PRIDEiQ49A26
ProteomicsDBi62016
62017 [Q49A26-2]
62018 [Q49A26-3]
62019 [Q49A26-4]
62020 [Q49A26-5]
TopDownProteomicsiQ49A26-2 [Q49A26-2]

PTM databases

iPTMnetiQ49A26
PhosphoSitePlusiQ49A26

Expressioni

Gene expression databases

BgeeiENSG00000140632 Expressed in 228 organ(s), highest expression level in right uterine tube
ExpressionAtlasiQ49A26 baseline and differential
GenevisibleiQ49A26 HS

Organism-specific databases

HPAiCAB017022
HPA048226
HPA050136

Interactioni

Subunit structurei

Interacts with MAPK14 (PubMed:16352664, Ref. 18). Interacts with KDM1B at nucleosomes; this interaction stimulates H3K4me1 and H3K4me2 demethylation (PubMed:23260659).3 Publications

Binary interactionsi

GO - Molecular functioni

Protein-protein interaction databases

BioGridi124176, 82 interactors
IntActiQ49A26, 270 interactors
MINTiQ49A26
STRINGi9606.ENSP00000322716

Structurei

Secondary structure

1553
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliQ49A26
SMRiQ49A26
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ49A26

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini8 – 66PWWPPROSITE-ProRule annotationAdd BLAST59

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni214 – 217Interaction with histone H31 Publication4
Regioni216 – 225Interaction with KDM1BCombined sources1 Publication10

Domaini

The A.T hook DNA-binding domain is required for the interaction with MAPK14.Curated
The PWWP domain probably mediates the binding to H3K36me3.1 Publication

Sequence similaritiesi

Belongs to the HIBADH-related family. NP60 subfamily.Curated

Phylogenomic databases

eggNOGiKOG0409 Eukaryota
KOG1904 Eukaryota
COG2084 LUCA
GeneTreeiENSGT00530000063270
InParanoidiQ49A26
OrthoDBiEOG091G0MNC
PhylomeDBiQ49A26
TreeFamiTF324195

Family and domain databases

CDDicd05836 N_Pac_NP60, 1 hit
Gene3Di1.10.1040.10, 1 hit
InterProiView protein in InterPro
IPR008927 6-PGluconate_DH-like_C_sf
IPR013328 6PGD_dom2
IPR006115 6PGDH_NADP-bd
IPR036291 NAD(P)-bd_dom_sf
IPR029154 NADP-bd
IPR035501 NP60_PWWP
IPR000313 PWWP_dom
PfamiView protein in Pfam
PF14833 NAD_binding_11, 1 hit
PF03446 NAD_binding_2, 1 hit
PF00855 PWWP, 1 hit
SMARTiView protein in SMART
SM00293 PWWP, 1 hit
SUPFAMiSSF48179 SSF48179, 1 hit
SSF51735 SSF51735, 1 hit
PROSITEiView protein in PROSITE
PS50812 PWWP, 1 hit

Sequences (5+)i

Sequence statusi: Complete.

This entry describes 5 isoformsi produced by alternative splicing. AlignAdd to basket

This entry has 5 described isoforms and 5 potential isoforms that are computationally mapped.Show allAlign All

Isoform 1 (identifier: Q49A26-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide
        10         20         30         40         50
MAAVSLRLGD LVWGKLGRYP PWPGKIVNPP KDLKKPRGKK CFFVKFFGTE
60 70 80 90 100
DHAWIKVEQL KPYHAHKEEM IKINKGKRFQ QAVDAVEEFL RRAKGKDQTS
110 120 130 140 150
SHNSSDDKNR RNSSEERSRP NSGDEKRKLS LSEGKVKKNM GEGKKRVSSG
160 170 180 190 200
SSERGSKSPL KRAQEQSPRK RGRPPKDEKD LTIPESSTVK GMMAGPMAAF
210 220 230 240 250
KWQPTASEPV KDADPHFHHF LLSQTEKPAV CYQAITKKLK ICEEETGSTS
260 270 280 290 300
IQAADSTAVN GSITPTDKKI GFLGLGLMGS GIVSNLLKMG HTVTVWNRTA
310 320 330 340 350
EKCDLFIQEG ARLGRTPAEV VSTCDITFAC VSDPKAAKDL VLGPSGVLQG
360 370 380 390 400
IRPGKCYVDM STVDADTVTE LAQVIVSRGG RFLEAPVSGN QQLSNDGMLV
410 420 430 440 450
ILAAGDRGLY EDCSSCFQAM GKTSFFLGEV GNAAKMMLIV NMVQGSFMAT
460 470 480 490 500
IAEGLTLAQV TGQSQQTLLD ILNQGQLASI FLDQKCQNIL QGNFKPDFYL
510 520 530 540 550
KYIQKDLRLA IALGDAVNHP TPMAAAANEV YKRAKALDQS DNDMSAVYRA

YIH
Length:553
Mass (Da):60,547
Last modified:October 10, 2018 - v4
Checksum:i2327FC8164B338B7
GO
Isoform 2 (identifier: Q49A26-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     228-244: Missing.

Note: No experimental confirmation available.
Show »
Length:536
Mass (Da):58,628
Checksum:i9CCE717C5FCA4462
GO
Isoform 5 (identifier: Q49A26-5) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     99-179: Missing.

Note: No experimental confirmation available.
Show »
Length:472
Mass (Da):51,499
Checksum:iB1F332409D1A403A
GO
Isoform 3 (identifier: Q49A26-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     303-308: Missing.

Note: No experimental confirmation available.
Show »
Length:547
Mass (Da):59,828
Checksum:iC7D785CCBF83204A
GO
Isoform 4 (identifier: Q49A26-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-69: Missing.

Note: No experimental confirmation available.
Show »
Length:484
Mass (Da):52,550
Checksum:iDB917C72DEB0E38F
GO

Computationally mapped potential isoform sequencesi

There are 5 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
K7EMM8K7EMM8_HUMAN
Putative oxidoreductase GLYR1
GLYR1
524Annotation score:
K7EQB2K7EQB2_HUMAN
Putative oxidoreductase GLYR1
GLYR1
185Annotation score:
K7ELL0K7ELL0_HUMAN
Putative oxidoreductase GLYR1
GLYR1
52Annotation score:
K7EPU6K7EPU6_HUMAN
Putative oxidoreductase GLYR1
GLYR1
171Annotation score:
K7EK70K7EK70_HUMAN
Putative oxidoreductase GLYR1
GLYR1
37Annotation score:

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti40K → E in AAH32855 (PubMed:15489334).Curated1
Sequence conflicti419A → T in AAH47223 (PubMed:15489334).Curated1
Sequence conflicti463Q → R in AAH47223 (PubMed:15489334).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_037403103N → D. Corresponds to variant dbSNP:rs34176249Ensembl.1
Natural variantiVAR_037404459Q → H. Corresponds to variant dbSNP:rs2085329Ensembl.1
Natural variantiVAR_037405531Y → C. Corresponds to variant dbSNP:rs17703111Ensembl.1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0297061 – 69Missing in isoform 4. 1 PublicationAdd BLAST69
Alternative sequenceiVSP_03822299 – 179Missing in isoform 5. 1 PublicationAdd BLAST81
Alternative sequenceiVSP_029707228 – 244Missing in isoform 2. 1 PublicationAdd BLAST17
Alternative sequenceiVSP_029708303 – 308Missing in isoform 3. 1 Publication6

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY352585 mRNA Translation: AAQ57265.1
AF244907 mRNA Translation: AAQ14242.1
AF326966 mRNA Translation: AAK15524.1
AK296842 mRNA Translation: BAG59409.1
AC020663 Genomic DNA No translation available.
CH471112 Genomic DNA Translation: EAW85252.1
CH471112 Genomic DNA Translation: EAW85257.1
BC003693 mRNA Translation: AAH03693.1
BC032855 mRNA Translation: AAH32855.1
BC047223 mRNA Translation: AAH47223.1
BC064940 mRNA Translation: AAH64940.1
CCDSiCCDS10524.1 [Q49A26-1]
CCDS81945.1 [Q49A26-3]
RefSeqiNP_001295025.1, NM_001308096.1
NP_115958.2, NM_032569.3
XP_011521019.1, XM_011522717.1
UniGeneiHs.387255
Hs.731580

Genome annotation databases

EnsembliENST00000321919; ENSP00000322716; ENSG00000140632 [Q49A26-1]
ENST00000436648; ENSP00000390276; ENSG00000140632 [Q49A26-5]
ENST00000591451; ENSP00000468328; ENSG00000140632 [Q49A26-3]
GeneIDi84656
KEGGihsa:84656
UCSCiuc002cxx.5 human [Q49A26-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Similar proteinsi

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY352585 mRNA Translation: AAQ57265.1
AF244907 mRNA Translation: AAQ14242.1
AF326966 mRNA Translation: AAK15524.1
AK296842 mRNA Translation: BAG59409.1
AC020663 Genomic DNA No translation available.
CH471112 Genomic DNA Translation: EAW85252.1
CH471112 Genomic DNA Translation: EAW85257.1
BC003693 mRNA Translation: AAH03693.1
BC032855 mRNA Translation: AAH32855.1
BC047223 mRNA Translation: AAH47223.1
BC064940 mRNA Translation: AAH64940.1
CCDSiCCDS10524.1 [Q49A26-1]
CCDS81945.1 [Q49A26-3]
RefSeqiNP_001295025.1, NM_001308096.1
NP_115958.2, NM_032569.3
XP_011521019.1, XM_011522717.1
UniGeneiHs.387255
Hs.731580

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2UYYX-ray2.50A/B/C/D261-553[»]
4GURX-ray2.51B152-268[»]
4GUSX-ray2.23B152-268[»]
4GUTX-ray2.00B152-268[»]
4GUUX-ray2.30B152-268[»]
4HSUX-ray1.99B152-268[»]
ProteinModelPortaliQ49A26
SMRiQ49A26
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi124176, 82 interactors
IntActiQ49A26, 270 interactors
MINTiQ49A26
STRINGi9606.ENSP00000322716

PTM databases

iPTMnetiQ49A26
PhosphoSitePlusiQ49A26

Polymorphism and mutation databases

BioMutaiGLYR1
DMDMi269849681

Proteomic databases

EPDiQ49A26
MaxQBiQ49A26
PaxDbiQ49A26
PeptideAtlasiQ49A26
PRIDEiQ49A26
ProteomicsDBi62016
62017 [Q49A26-2]
62018 [Q49A26-3]
62019 [Q49A26-4]
62020 [Q49A26-5]
TopDownProteomicsiQ49A26-2 [Q49A26-2]

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000321919; ENSP00000322716; ENSG00000140632 [Q49A26-1]
ENST00000436648; ENSP00000390276; ENSG00000140632 [Q49A26-5]
ENST00000591451; ENSP00000468328; ENSG00000140632 [Q49A26-3]
GeneIDi84656
KEGGihsa:84656
UCSCiuc002cxx.5 human [Q49A26-1]

Organism-specific databases

CTDi84656
DisGeNETi84656
EuPathDBiHostDB:ENSG00000140632.16
GeneCardsiGLYR1
HGNCiHGNC:24434 GLYR1
HPAiCAB017022
HPA048226
HPA050136
MIMi610660 gene
neXtProtiNX_Q49A26
OpenTargetsiENSG00000140632
PharmGKBiPA165450093
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG0409 Eukaryota
KOG1904 Eukaryota
COG2084 LUCA
GeneTreeiENSGT00530000063270
InParanoidiQ49A26
OrthoDBiEOG091G0MNC
PhylomeDBiQ49A26
TreeFamiTF324195

Miscellaneous databases

ChiTaRSiGLYR1 human
EvolutionaryTraceiQ49A26
GenomeRNAii84656
PROiPR:Q49A26
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000140632 Expressed in 228 organ(s), highest expression level in right uterine tube
ExpressionAtlasiQ49A26 baseline and differential
GenevisibleiQ49A26 HS

Family and domain databases

CDDicd05836 N_Pac_NP60, 1 hit
Gene3Di1.10.1040.10, 1 hit
InterProiView protein in InterPro
IPR008927 6-PGluconate_DH-like_C_sf
IPR013328 6PGD_dom2
IPR006115 6PGDH_NADP-bd
IPR036291 NAD(P)-bd_dom_sf
IPR029154 NADP-bd
IPR035501 NP60_PWWP
IPR000313 PWWP_dom
PfamiView protein in Pfam
PF14833 NAD_binding_11, 1 hit
PF03446 NAD_binding_2, 1 hit
PF00855 PWWP, 1 hit
SMARTiView protein in SMART
SM00293 PWWP, 1 hit
SUPFAMiSSF48179 SSF48179, 1 hit
SSF51735 SSF51735, 1 hit
PROSITEiView protein in PROSITE
PS50812 PWWP, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiGLYR1_HUMAN
AccessioniPrimary (citable) accession number: Q49A26
Secondary accession number(s): B4DL47
, C9JJ40, C9JJ60, Q5U632, Q6P1Q2, Q6V3W7, Q9BTI1, Q9BXK2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 4, 2007
Last sequence update: October 10, 2018
Last modified: November 7, 2018
This is version 130 of the entry and version 4 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families
  2. Human chromosome 16
    Human chromosome 16: entries, gene names and cross-references to MIM
  3. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  4. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  5. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  6. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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