Reviewed, UniProtKB/Swiss-Prot P78330 (SERB_HUMAN)

Names and origin

Protein names

Recommended name:
    Phosphoserine phosphatase
      Short name=PSPase
      Short name=PSP
    EC=3.1.3.3
Alternative name(s):
    O-phosphoserine phosphohydrolase
    L-3-phosphoserine phosphatase

Gene names

Name:

PSPH

Organism

Homo sapiens (Human) [Complete proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	225 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Catalyzes the last step in the biosynthesis of serine from carbohydrates. The reaction mechanism proceeds via the formation of a phosphoryl-enzyme intermediates.
Catalytic activity	O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate.
Cofactor	Magnesium.
Pathway	Amino-acid biosynthesis; L-serine biosynthesis; L-serine from 3-phospho-D-glycerate: step 3/3.
Subunit structure	Homodimer.
Involvement in disease	Defects in PSPH are the cause of 3-phosphoserine phosphatase deficiency (PSPHD)[MIM:172480]. Affected individuals have pre- and postnatal growth retardation, moderate psychomotor retardation and facial features suggestive of Williams syndrome. Ref.8
Sequence similarities	Belongs to the serB family.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis Serine biosynthesis
Disease	Disease mutation
Ligand	Magnesium
Molecular function	Hydrolase
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	L-serine biosynthetic process Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW phosphoserine phosphatase activity Ref.8 Inferred from direct assay. Source: UniProtKB protein binding Inferred from physical interaction. Source: IntAct
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ASF1B	Q9NVP2	1	EBI-1042956,EBI-1055650
PRPSAP1	Q14558	1	EBI-1042956,EBI-724449
STYXL1	Q9Y6J8	1	EBI-1042956,EBI-1044511

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 225

225

Phosphoserine phosphatase

PRO_0000156879

Amino acid modifications

Modified residue

1

1

N-acetylmethionine Ref.7

Natural variations

Natural variant

32

1

D → N in PSPHD. dbSNP rs28933976. Ref.8

VAR_022378

Natural variant

52

1

M → T in PSPHD. Ref.8

VAR_022379

Experimental info

Sequence conflict

2

1

V → I in CAA71318. Ref.1

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

225

Helix Strand Turn

Details...

Helix

6 – 13

8

Beta strand

15 – 20

6

Turn

23 – 25

3

Beta strand

26 – 28

3

Helix

30 – 37

8

Turn

41 – 43

3

Helix

58 – 69

12

Helix

73 – 82

10

Helix

91 – 100

10

Beta strand

104 – 112

9

Helix

113 – 122

10

Helix

127 – 129

3

Beta strand

130 – 133

4

Beta strand

135 – 138

4

Beta strand

143 – 146

4

Helix

151 – 153

3

Helix

157 – 169

13

Beta strand

174 – 180

7

Helix

181 – 184

4

Turn

185 – 189

5

Beta strand

190 – 196

7

Helix

203 – 208

6

Beta strand

210 – 214

5

Helix

216 – 219

4

Sequences

	Sequence		Length	Mass (Da)
	P78330-1 [UniParc]. Last modified April 26, 2005. Version 2. Checksum: BD5D72697747FA30	FASTA	225	25,008
	10 20 30 40 50 60 MVSHSELRKL FYSADAVCFD VDSTVIREEG IDELAKICGV EDAVSEMTRR AMGGAVPFKA 70 80 90 100 110 120 ALTERLALIQ PSREQVQRLI AEQPPHLTPG IRELVSRLQE RNVQVFLISG GFRSIVEHVA 130 140 150 160 170 180 SKLNIPATNV FANRLKFYFN GEYAGFDETQ PTAESGGKGK VIKLLKEKFH FKKIIMIGDG 190 200 210 220 ATDMEACPPA DAFIGFGGNV IRQQVKDNAK WYITDFVELL GELEE

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate." Collet J.-F., Gerin I., Rider M.H., Veiga-Da-Cunha M., Van Schaftingen E. FEBS Lett. 408:281-284(1997) [PubMed: 9188776] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]	"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]. Tissue: Kidney.
[3]	"The full-ORF clone resource of the German cDNA consortium." Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I. BMC Genomics 8:399-399(2007) [PubMed: 17974005] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Tissue: Endometrial tumor.
[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].
[6]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
[7]	"Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach." Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S. Anal. Chem. 81:4493-4501(2009) [PubMed: 19413330] [Abstract] Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, MASS SPECTROMETRY.
[8]	"Mutations responsible for 3-phosphoserine phosphatase deficiency." Veiga-da-Cunha M., Collet J.F., Prieur B., Jaeken J., Peeraer Y., Rabbijns A., Van Schaftingen E. Eur. J. Hum. Genet. 12:163-166(2004) [PubMed: 14673469] [Abstract] Cited for: VARIANTS PSPHD ASN-32 AND THR-52.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Y10275 mRNA. Translation: CAA71318.1.
AK315235 mRNA. Translation: BAG37662.1.
BX537439 mRNA. Translation: CAD97681.1.
CH471140 Genomic DNA. Translation: EAX07968.1.
BC063614 mRNA. Translation: AAH63614.1.

IPI

IPI00019178.

RefSeq

NP_004568.2.

UniGene

Hs.512656

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1L8L	X-ray	2.51	A/B	3-225	[»]
1L8O	X-ray	2.80	A/B	3-225	[»]
1NNL	X-ray	1.53	A/B	3-225	[»]

ModBase

Search...

Protein-protein interaction databases

IntAct

P78330. 16 interactions.

STRING

P78330.

PTM databases

PhosphoSite

P78330.

Proteomic databases

PeptideAtlas

P78330.

PRIDE

P78330.

Genome annotation databases

Ensembl

ENST00000275605; ENSP00000275605; ENSG00000146733; Homo sapiens. [Genome view]
ENST00000395471; ENSP00000378854; ENSG00000146733; Homo sapiens. [Genome view]
ENST00000437355; ENSP00000401639; ENSG00000146733; Homo sapiens. [Genome view]

GeneID

5723.

KEGG

hsa:5723.

UCSC

uc003trg.1. human.

Organism-specific databases

CTD

5723.

GeneCards

GC07M056046.

H-InvDB

HIX0021579.
HIX0058416.

HGNC

HGNC:9577. PSPH.

HPA

HPA020376.

MIM

172480. gene+phenotype.

Orphanet

35705. Neurometabolic disorder due to serine deficiency.

PharmGKB

PA33928.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG17027.

HOGENOM

HBG482410.

HOVERGEN

P78330.

InParanoid

P78330.

OMA

PATNVFA.

OrthoDB

EOG95TG6X.

PhylomeDB

P78330.

Enzyme and pathway databases

BRENDA

3.1.3.3. 247.

Gene expression databases

ArrayExpress

P78330.

Bgee

P78330.

CleanEx

HS_PSPH.

Genevestigator

P78330.

GermOnline

ENSG00000146733. Homo sapiens.

Family and domain databases

InterPro

IPR005834. Dehalogen-like_hydro.
IPR006383. HAD-SF_hydro_IB_PSP-like.
IPR004469. SerB.
[Graphical view]

Pfam

PF00702. Hydrolase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01488. HAD-SF-IB. 1 hit.
TIGR00338. serB. 1 hit.

ProtoNet

Search...

Other Resources

NextBio

22244.

SOURCE

Search...

Entry information

Entry name

SERB_HUMAN

Accession

Primary (citable) accession number: P78330
Secondary accession number(s): B2RCR5, Q7Z3S5

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	April 26, 2005
Last modified:	February 9, 2010
This is version 94 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)

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.