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Q08623 (HDHD1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 114. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Pseudouridine-5'-monophosphatase

Short name=5'-PsiMPase
EC=3.1.3.n6
Alternative name(s):
Haloacid dehalogenase-like hydrolase domain-containing protein 1
Haloacid dehalogenase-like hydrolase domain-containing protein 1A
Protein GS1
Gene names
Name:HDHD1
Synonyms:DXF68S1E, FAM16AX, GS1, HDHD1A
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length228 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Dephosphorylates pseudouridine 5'-phosphate, a potential intermediate in rRNA degradation. Pseudouridine is then excreted intact in urine. Ref.7

Catalytic activity

pseudouridine 5'-monophosphate + H2O = Pseudouridine + phosphate. Ref.7

Cofactor

Magnesium. Ref.7

Induction

Inhibited by low concentrations of calcium.

Sequence similarities

Belongs to the HAD-like hydrolase superfamily. CbbY/CbbZ/Gph/YieH family.

Biophysicochemical properties

Kinetic parameters:

KM=0.38 µM for 5'-PsiMP Ref.7

KM=1.5 mM for 3'-AMP

KM=5.9 mM for Fructose-6-P

KM=9.4 mM for 5'-UMP

Sequence caution

The sequence AAA58622.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence AAH12494.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence BAD97125.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

The sequence BAG35973.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
   Biological processNucleotide metabolism
   Coding sequence diversityAlternative splicing
Polymorphism
   LigandMagnesium
Metal-binding
   Molecular functionHydrolase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processnucleotide metabolic process

Inferred from electronic annotation. Source: UniProtKB-KW

   Molecular_functionmetal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

phosphatase activity

Inferred from electronic annotation. Source: UniProtKB-EC

Complete GO annotation...

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q08623-1)

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.
Isoform 2 (identifier: Q08623-2)

The sequence of this isoform differs from the canonical sequence as follows:
     51-93: Missing.
Note: No experimental confirmation available.
Isoform 3 (identifier: Q08623-3)

The sequence of this isoform differs from the canonical sequence as follows:
     171-228: CLVFEDAPNG...PELFGLPSYE → SSIHRPRLLT...NQLLLCSDDT
Note: No experimental confirmation available.
Isoform 4 (identifier: Q08623-4)

The sequence of this isoform differs from the canonical sequence as follows:
     20-20: L → LGYTGSIVAAASGESSRGLQSRWT
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 228228Pseudouridine-5'-monophosphatase
PRO_0000108068

Sites

Active site141Nucleophile By similarity
Active site161Proton donor By similarity
Metal binding141Magnesium By similarity
Metal binding161Magnesium By similarity

Natural variations

Alternative sequence201L → LGYTGSIVAAASGESSRGLQ SRWT in isoform 4.
VSP_044804
Alternative sequence51 – 9343Missing in isoform 2.
VSP_040029
Alternative sequence171 – 22858CLVFE…LPSYE → SSIHRPRLLTAQKCQGCRDP FSALLLLCNQLLLCSDDT in isoform 3.
VSP_042020
Natural variant881T → M. Ref.1 Ref.6
Corresponds to variant rs1131197 [ dbSNP | Ensembl ].
VAR_061094
Natural variant1651P → A.
Corresponds to variant rs3747386 [ dbSNP | Ensembl ].
VAR_060625

Experimental info

Sequence conflict1161G → R in AAH12494. Ref.5
Sequence conflict1531D → G in BAD97125. Ref.1
Sequence conflict1911V → A in AAA58622. Ref.6
Isoform 3:
Sequence conflict1981C → S in BAH13339. Ref.1

Secondary structure

.......................................... 228
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified November 24, 2009. Version 3.
Checksum: EF9B8CC51C122924

FASTA22825,249
        10         20         30         40         50         60 
MAAPPQPVTH LIFDMDGLLL DTERLYSVVF QEICNRYDKK YSWDVKSLVM GKKALEAAQI 

        70         80         90        100        110        120 
IIDVLQLPMS KEELVEESQT KLKEVFPTAA LMPGAEKLII HLRKHGIPFA LATSSGSASF 

       130        140        150        160        170        180 
DMKTSRHKEF FSLFSHIVLG DDPEVQHGKP DPDIFLACAK RFSPPPAMEK CLVFEDAPNG 

       190        200        210        220 
VEAALAAGMQ VVMVPDGNLS RDLTTKATLV LNSLQDFQPE LFGLPSYE 

« Hide

Isoform 2 [UniParc].

Checksum: 6AEAE431AC9D25BB
Show »

FASTA18520,529
Isoform 3 [UniParc].

Checksum: 9BE317B82AA8FF15
Show »

FASTA20823,283
Isoform 4 [UniParc].

Checksum: 8671CFD416181D12
Show »

FASTA25127,573

References

« Hide 'large scale' references
[1]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1; 2 AND 3), VARIANT MET-88.
Tissue: Fetal brain, Neuroepithelioma and Small intestine.
[2]Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Liver cancer.
[3]"The DNA sequence of the human X chromosome."
Ross M.T., Grafham D.V., Coffey A.J., Scherer S., McLay K., Muzny D., Platzer M., Howell G.R., Burrows C., Bird C.P., Frankish A., Lovell F.L., Howe K.L., Ashurst J.L., Fulton R.S., Sudbrak R., Wen G., Jones M.C. expand/collapse author list , Hurles M.E., Andrews T.D., Scott C.E., Searle S., Ramser J., Whittaker A., Deadman R., Carter N.P., Hunt S.E., Chen R., Cree A., Gunaratne P., Havlak P., Hodgson A., Metzker M.L., Richards S., Scott G., Steffen D., Sodergren E., Wheeler D.A., Worley K.C., Ainscough R., Ambrose K.D., Ansari-Lari M.A., Aradhya S., Ashwell R.I., Babbage A.K., Bagguley C.L., Ballabio A., Banerjee R., Barker G.E., Barlow K.F., Barrett I.P., Bates K.N., Beare D.M., Beasley H., Beasley O., Beck A., Bethel G., Blechschmidt K., Brady N., Bray-Allen S., Bridgeman A.M., Brown A.J., Brown M.J., Bonnin D., Bruford E.A., Buhay C., Burch P., Burford D., Burgess J., Burrill W., Burton J., Bye J.M., Carder C., Carrel L., Chako J., Chapman J.C., Chavez D., Chen E., Chen G., Chen Y., Chen Z., Chinault C., Ciccodicola A., Clark S.Y., Clarke G., Clee C.M., Clegg S., Clerc-Blankenburg K., Clifford K., Cobley V., Cole C.G., Conquer J.S., Corby N., Connor R.E., David R., Davies J., Davis C., Davis J., Delgado O., Deshazo D., Dhami P., Ding Y., Dinh H., Dodsworth S., Draper H., Dugan-Rocha S., Dunham A., Dunn M., Durbin K.J., Dutta I., Eades T., Ellwood M., Emery-Cohen A., Errington H., Evans K.L., Faulkner L., Francis F., Frankland J., Fraser A.E., Galgoczy P., Gilbert J., Gill R., Gloeckner G., Gregory S.G., Gribble S., Griffiths C., Grocock R., Gu Y., Gwilliam R., Hamilton C., Hart E.A., Hawes A., Heath P.D., Heitmann K., Hennig S., Hernandez J., Hinzmann B., Ho S., Hoffs M., Howden P.J., Huckle E.J., Hume J., Hunt P.J., Hunt A.R., Isherwood J., Jacob L., Johnson D., Jones S., de Jong P.J., Joseph S.S., Keenan S., Kelly S., Kershaw J.K., Khan Z., Kioschis P., Klages S., Knights A.J., Kosiura A., Kovar-Smith C., Laird G.K., Langford C., Lawlor S., Leversha M., Lewis L., Liu W., Lloyd C., Lloyd D.M., Loulseged H., Loveland J.E., Lovell J.D., Lozado R., Lu J., Lyne R., Ma J., Maheshwari M., Matthews L.H., McDowall J., McLaren S., McMurray A., Meidl P., Meitinger T., Milne S., Miner G., Mistry S.L., Morgan M., Morris S., Mueller I., Mullikin J.C., Nguyen N., Nordsiek G., Nyakatura G., O'dell C.N., Okwuonu G., Palmer S., Pandian R., Parker D., Parrish J., Pasternak S., Patel D., Pearce A.V., Pearson D.M., Pelan S.E., Perez L., Porter K.M., Ramsey Y., Reichwald K., Rhodes S., Ridler K.A., Schlessinger D., Schueler M.G., Sehra H.K., Shaw-Smith C., Shen H., Sheridan E.M., Shownkeen R., Skuce C.D., Smith M.L., Sotheran E.C., Steingruber H.E., Steward C.A., Storey R., Swann R.M., Swarbreck D., Tabor P.E., Taudien S., Taylor T., Teague B., Thomas K., Thorpe A., Timms K., Tracey A., Trevanion S., Tromans A.C., d'Urso M., Verduzco D., Villasana D., Waldron L., Wall M., Wang Q., Warren J., Warry G.L., Wei X., West A., Whitehead S.L., Whiteley M.N., Wilkinson J.E., Willey D.L., Williams G., Williams L., Williamson A., Williamson H., Wilming L., Woodmansey R.L., Wray P.W., Yen J., Zhang J., Zhou J., Zoghbi H., Zorilla S., Buck D., Reinhardt R., Poustka A., Rosenthal A., Lehrach H., Meindl A., Minx P.J., Hillier L.W., Willard H.F., Wilson R.K., Waterston R.H., Rice C.M., Vaudin M., Coulson A., Nelson D.L., Weinstock G., Sulston J.E., Durbin R.M., Hubbard T., Gibbs R.A., Beck S., Rogers J., Bentley D.R.
Nature 434:325-337(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 4).
Tissue: Embryonic stem cell and Testis.
[6]"Isolation of a new gene from the distal short arm of the human X chromosome that escapes X-inactivation."
Yen P.H., Ellison J., Salido E.C., Mohandas T., Shapiro L.
Hum. Mol. Genet. 1:47-52(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 4-228 (ISOFORM 1), VARIANT MET-88.
[7]"HDHD1, which is often deleted in X-linked ichthyosis, encodes a pseudouridine-5'-phosphatase."
Preumont A., Rzem R., Vertommen D., Van Schaftingen E.
Biochem. J. 431:237-244(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, COFACTOR, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.
Tissue: Erythrocyte.
[8]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[9]"The crystal structure of human haloacid dehalogenase-like hydrolase domain containing 1A (HDHD1A)."
Structural genomics consortium (SGC)
Submitted (MAR-2010) to the PDB data bank
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS).

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK300985 mRNA. Translation: BAG62605.1.
AK313155 mRNA. Translation: BAG35973.1. Different initiation.
AK223405 mRNA. Translation: BAD97125.1. Different initiation.
AK300740 mRNA. Translation: BAH13339.1.
AC073583 Genomic DNA. No translation available.
CH471074 Genomic DNA. Translation: EAW98748.1.
BC012494 mRNA. Translation: AAH12494.1. Different initiation.
DR156836 mRNA. No translation available.
M86934 mRNA. Translation: AAA58622.1. Different initiation.
RefSeqNP_001129037.1. NM_001135565.1.
NP_001171606.1. NM_001178135.1.
NP_001171607.1. NM_001178136.1.
NP_036212.3. NM_012080.4.
UniGeneHs.185910.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3L5KX-ray2.00A1-228[»]
ProteinModelPortalQ08623.
SMRQ08623. Positions 1-228.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid113859. 1 interaction.
MINTMINT-5003687.

PTM databases

PhosphoSiteQ08623.

Polymorphism databases

DMDM269849688.

Proteomic databases

PaxDbQ08623.
PRIDEQ08623.

Protocols and materials databases

DNASU8226.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000381077; ENSP00000370467; ENSG00000130021. [Q08623-1]
ENST00000412827; ENSP00000406260; ENSG00000130021. [Q08623-2]
ENST00000424830; ENSP00000396452; ENSG00000130021. [Q08623-4]
ENST00000540122; ENSP00000441208; ENSG00000130021. [Q08623-3]
GeneID8226.
KEGGhsa:8226.
UCSCuc004crv.2. human. [Q08623-1]
uc011mhn.1. human. [Q08623-2]
uc011mho.1. human. [Q08623-3]

Organism-specific databases

CTD8226.
GeneCardsGC0XM006966.
HGNCHGNC:16818. HDHD1.
MIM306480. gene.
neXtProtNX_Q08623.
PharmGKBPA165756731.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0637.
HOGENOMHOG000248341.
HOVERGENHBG005917.
InParanoidQ08623.
KOK17623.
OMAERIYTEV.
OrthoDBEOG7TF79X.
PhylomeDBQ08623.
TreeFamTF105946.

Gene expression databases

ArrayExpressQ08623.
BgeeQ08623.
CleanExHS_HDHD1A.
GenevestigatorQ08623.

Family and domain databases

Gene3D3.40.50.1000. 2 hits.
InterProIPR023214. HAD-like_dom.
IPR006439. HAD-SF_hydro_IA.
[Graphical view]
PfamPF13419. HAD_2. 1 hit.
[Graphical view]
SUPFAMSSF56784. SSF56784. 1 hit.
TIGRFAMsTIGR01509. HAD-SF-IA-v3. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ08623.
GeneWikiHDHD1A.
GenomeRNAi8226.
NextBio30966.
PROQ08623.
SOURCESearch...

Entry information

Entry nameHDHD1_HUMAN
AccessionPrimary (citable) accession number: Q08623
Secondary accession number(s): B2R7X6 expand/collapse secondary AC list , B4DV93, B7Z6Q3, E9PAV8, F5GWZ2, Q53F84, Q96EB8
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1995
Last sequence update: November 24, 2009
Last modified: April 16, 2014
This is version 114 of the entry and version 3 of the sequence. [Complete history]
Entry statusReviewed (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.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome X

Human chromosome X: entries, gene names and cross-references to MIM