Q08623 (HDHD1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Homo sapiens (Human)

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo

Protein attributes

Sequence length	228 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	Nucleotide metabolism
Coding sequence diversity	Alternative splicing Polymorphism
Ligand	Magnesium Metal-binding
Molecular function	Hydrolase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological process	nucleotide metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphatase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Alternative products

This entry describes 3 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.
Sequence annotation (Features)
	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
	Sequence conflict	198	1	C → S in BAH13339. Ref.1

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 228

228

Pseudouridine-5'-monophosphatase

PRO_0000108068

Sites

Active site

14

1

Nucleophile By similarity

Active site

16

1

Proton donor By similarity

Metal binding

14

1

Magnesium By similarity

Metal binding

16

1

Magnesium By similarity

Natural variations

Alternative sequence

51 – 93

43

Missing in isoform 2.

VSP_040029

Alternative sequence

171 – 228

58

CLVFE…LPSYE → SSIHRPRLLTAQKCQGCRDP FSALLLLCNQLLLCSDDT in isoform 3.

VSP_042020

Natural variant

88

1

T → M. Ref.1 Ref.6
Corresponds to variant rs1131197 [ dbSNP | Ensembl ].

VAR_061094

Natural variant

165

1

P → A.
Corresponds to variant rs3747386 [ dbSNP | Ensembl ].

VAR_060625

Experimental info

Sequence conflict

116

1

G → R in AAH12494. Ref.5

Sequence conflict

153

1

D → G in BAD97125. Ref.1

Sequence conflict

191

1

V → A in AAA58622. Ref.6

Secondary structure

1

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228

Helix Strand Turn

Details...

Beta strand

1 – 3

3

Beta strand

9 – 14

6

Helix

22 – 36

15

Helix

43 – 49

7

Helix

54 – 65

12

Helix

71 – 85

15

Helix

86 – 88

3

Helix

96 – 104

9

Beta strand

109 – 112

4

Helix

117 – 123

7

Turn

124 – 126

3

Helix

128 – 131

4

Helix

153 – 160

8

Beta strand

162 – 164

3

Helix

168 – 170

3

Beta strand

171 – 177

7

Helix

182 – 186

5

Beta strand

190 – 193

4

Helix

201 – 203

3

Beta strand

207 – 210

4

Helix

214 – 216

3

Helix

219 – 221

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified November 24, 2009. Version 3. Checksum: EF9B8CC51C122924	FASTA	228	25,249
	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
	Isoform 2 [UniParc]. Checksum: 6AEAE431AC9D25BB	FASTA	185	20,529
	10 20 30 40 50 60 MAAPPQPVTH LIFDMDGLLL DTERLYSVVF QEICNRYDKK YSWDVKSLVM GAEKLIIHLR 70 80 90 100 110 120 KHGIPFALAT SSGSASFDMK TSRHKEFFSL FSHIVLGDDP EVQHGKPDPD IFLACAKRFS 130 140 150 160 170 180 PPPAMEKCLV FEDAPNGVEA ALAAGMQVVM VPDGNLSRDL TTKATLVLNS LQDFQPELFG LPSYE
	Isoform 3 [UniParc]. Checksum: 9BE317B82AA8FF15	FASTA	208	23,283
	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 SSIHRPRLLT 190 200 AQKCQGCRDP FSALLLLCNQ LLLCSDDT

References

	« Hide 'large scale' referencesShow '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. , 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: 14702039] [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. , 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: 15772651] [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. , 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: 15489334] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1). Tissue: 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: 1284467] [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: 20722631] [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: 21269460] [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.
M86934 mRNA. Translation: AAA58622.1. Different initiation.

IPI

IPI00302436.
IPI00908643.

RefSeq

NP_001129037.1. NM_001135565.1.
NP_001171606.1. NM_001178135.1.
NP_001171607.1. NM_001178136.1.
NP_036212.3. NM_012080.4.

UniGene

Hs.185910.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3L5K	X-ray	2.00	A	1-228	[»]

ProteinModelPortal

Q08623.

SMR

Q08623. Positions 1-228.

ModBase

Search...

Protein-protein interaction databases

STRING

Q08623.

PTM databases

PhosphoSite

Q08623.

Polymorphism databases

DMDM

269849688.

Proteomic databases

PRIDE

Q08623.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000381077; ENSP00000370467; ENSG00000130021.
ENST00000412827; ENSP00000406260; ENSG00000130021.

GeneID

8226.

KEGG

hsa:8226.

NMPDR

fig|9606.3.peg.32410.

UCSC

uc004crv.1. human.

Organism-specific databases

CTD

8226.

GeneCards

GC0XM006966.

H-InvDB

HIX0016639.

HGNC

HGNC:16818. HDHD1.

MIM

306480. gene.

neXtProt

NX_Q08623.

PharmGKB

PA128394539.
PA165756731.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG06037.

GeneTree

ENSGT00390000014753.

HOVERGEN

HBG005917.

InParanoid

Q08623.

OrthoDB

EOG46MBKM.

PhylomeDB

Q08623.

Gene expression databases

ArrayExpress

Q08623.

Bgee

Q08623.

CleanEx

HS_HDHD1A.

Genevestigator

Q08623.

GermOnline

ENSG00000130021. Homo sapiens.

Family and domain databases

InterPro

IPR005834. Dehalogen-like_hydro.
IPR023214. HAD-like_dom.
IPR006402. HAD-SF_hydro_IA_v3.
[Graphical view]

Gene3D

G3DSA:3.40.50.1000. HAD-like_dom. 2 hits.

Pfam

PF00702. Hydrolase. 1 hit.
[Graphical view]

SUPFAM

SSF56784. HAD-like_dom. 1 hit.

TIGRFAMs

TIGR01509. HAD-SF-IA-v3. 1 hit.

ProtoNet

Search...

Other

NextBio

30966.

SOURCE

Search...

Entry information

Entry name

HDHD1_HUMAN

Accession

Primary (citable) accession number: Q08623
Secondary accession number(s): B2R7X6 , B4DV93, B7Z6Q3, F5GWZ2, Q53F84, Q96EB8

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 1, 1995
Last sequence update:	November 24, 2009
Last modified:	January 25, 2012
This is version 90 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.