Reviewed, UniProtKB/Swiss-Prot Q96GD0 (PLPP_HUMAN)

Names and origin

Protein names

Recommended name:
    Pyridoxal phosphate phosphatase
      Short name=PLP phosphatase
    EC=3.1.3.74

Gene names

Name:	PDXP
Synonyms:	PLP, PLPP

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	296 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Pyridoxal phosphate phosphatase. Has some activity towards pyridoxal 5'-phosphate (PLP), pyridoxine 5'-phosphate (PMP) and Pyridoxine 5'-phosphate (PNP), with a highest activity with PLP followed by PNP. Ref.1
Catalytic activity	Pyridoxal 5'-phosphate + H2O = pyridoxal + phosphate. Ref.5
Cofactor	Divalent ions. Magnesium is the most effective. Ref.1
Subunit structure	Homodimer. Ref.1
Tissue specificity	Ubiquitous. Highly expressed in all the regions of central nerve system except the spinal cord. Also expressed at high level in liver and testis. In fetus, it is weakly expressed in all organs except brain. Ref.1
Sequence similarities	Belongs to the HAD-like hydrolase superfamily.

Ontologies

Keywords
Ligand	Magnesium Metal-binding Pyridoxal phosphate
Molecular function	Hydrolase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	metabolic process Inferred from electronic annotation. Source: InterPro
Cellular component	cytoplasm Inferred from direct assay. Source: HPA nucleus Inferred from direct assay. Source: HPA
Molecular function	magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW pyridoxal phosphatase activity Inferred from electronic annotation. Source: EC
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 296

296

Pyridoxal phosphate phosphatase

PRO_0000068837

Sites

Active site

25

1

Nucleophile By similarity

Active site

27

1

Proton donor By similarity

Metal binding

25

1

Magnesium By similarity

Metal binding

27

1

Magnesium By similarity

Metal binding

238

1

Magnesium By similarity

Secondary structure

1

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296

Helix Strand Turn

Details...

Helix

9 – 18

10

Beta strand

20 – 24

5

Turn

27 – 29

3

Beta strand

30 – 32

3

Helix

40 – 49

10

Beta strand

53 – 58

6

Helix

65 – 74

10

Helix

82 – 84

3

Beta strand

85 – 87

3

Helix

88 – 99

12

Beta strand

109 – 114

6

Helix

116 – 124

9

Beta strand

143 – 148

6

Helix

156 – 165

10

Beta strand

171 – 176

6

Beta strand

181 – 183

3

Beta strand

189 – 191

3

Helix

193 – 204

12

Helix

217 – 222

6

Turn

223 – 225

3

Helix

230 – 232

3

Beta strand

233 – 238

6

Turn

240 – 242

3

Helix

243 – 250

8

Beta strand

253 – 257

5

Helix

264 – 272

9

Helix

276 – 278

3

Beta strand

281 – 286

6

Helix

287 – 289

3

Helix

291 – 294

4

Sequences

	Sequence		Length	Mass (Da)
	Q96GD0-1 [UniParc]. Last modified March 1, 2004. Version 2. Checksum: 33466C35A76B458C	FASTA	296	31,698
	10 20 30 40 50 60 MARCERLRGA ALRDVLGRAQ GVLFDCDGVL WNGERAVPGA PELLERLARA GKAALFVSNN 70 80 90 100 110 120 SRRARPELAL RFARLGFGGL RAEQLFSSAL CAARLLRQRL PGPPDAPGAV FVLGGEGLRA 130 140 150 160 170 180 ELRAAGLRLA GDPSAGDGAA PRVRAVLVGY DEHFSFAKLR EACAHLRDPE CLLVATDRDP 190 200 210 220 230 240 WHPLSDGSRT PGTGSLAAAV ETASGRQALV VGKPSPYMFE CITENFSIDP ARTLMVGDRL 250 260 270 280 290 ETDILFGHRC GMTTVLTLTG VSRLEEAQAY LAAGQHDLVP HYYVESIADL TEGLED

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Human pyridoxal phosphatase. Molecular cloning, functional expression, and tissue distribution." Jang Y.M., Kim D.W., Kang T.-C., Won M.H., Baek N.-I., Moon B.J., Choi S.Y., Kwon O.-S. J. Biol. Chem. 278:50040-50046(2003) [PubMed: 14522954] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, HOMODIMERIZATION, COFACTOR, SUBUNIT, TISSUE SPECIFICITY. Tissue: Brain.
[2]	"The DNA sequence of human chromosome 22." Dunham I., Hunt A.R., Collins J.E., Bruskiewich R., Beare D.M., Clamp M., Smink L.J., Ainscough R., Almeida J.P., Babbage A.K., Bagguley C., Bailey J., Barlow K.F., Bates K.N., Beasley O.P., Bird C.P., Blakey S.E., Bridgeman A.M. , Buck D., Burgess J., Burrill W.D., Burton J., Carder C., Carter N.P., Chen Y., Clark G., Clegg S.M., Cobley V.E., Cole C.G., Collier R.E., Connor R., Conroy D., Corby N.R., Coville G.J., Cox A.V., Davis J., Dawson E., Dhami P.D., Dockree C., Dodsworth S.J., Durbin R.M., Ellington A.G., Evans K.L., Fey J.M., Fleming K., French L., Garner A.A., Gilbert J.G.R., Goward M.E., Grafham D.V., Griffiths M.N.D., Hall C., Hall R.E., Hall-Tamlyn G., Heathcott R.W., Ho S., Holmes S., Hunt S.E., Jones M.C., Kershaw J., Kimberley A.M., King A., Laird G.K., Langford C.F., Leversha M.A., Lloyd C., Lloyd D.M., Martyn I.D., Mashreghi-Mohammadi M., Matthews L.H., Mccann O.T., Mcclay J., Mclaren S., McMurray A.A., Milne S.A., Mortimore B.J., Odell C.N., Pavitt R., Pearce A.V., Pearson D., Phillimore B.J.C.T., Phillips S.H., Plumb R.W., Ramsay H., Ramsey Y., Rogers L., Ross M.T., Scott C.E., Sehra H.K., Skuce C.D., Smalley S., Smith M.L., Soderlund C., Spragon L., Steward C.A., Sulston J.E., Swann R.M., Vaudin M., Wall M., Wallis J.M., Whiteley M.N., Willey D.L., Williams L., Williams S.A., Williamson H., Wilmer T.E., Wilming L., Wright C.L., Hubbard T., Bentley D.R., Beck S., Rogers J., Shimizu N., Minoshima S., Kawasaki K., Sasaki T., Asakawa S., Kudoh J., Shintani A., Shibuya K., Yoshizaki Y., Aoki N., Mitsuyama S., Roe B.A., Chen F., Chu L., Crabtree J., Deschamps S., Do A., Do T., Dorman A., Fang F., Fu Y., Hu P., Hua A., Kenton S., Lai H., Lao H.I., Lewis J., Lewis S., Lin S.-P., Loh P., Malaj E., Nguyen T., Pan H., Phan S., Qi S., Qian Y., Ray L., Ren Q., Shaull S., Sloan D., Song L., Wang Q., Wang Y., Wang Z., White J., Willingham D., Wu H., Yao Z., Zhan M., Zhang G., Chissoe S., Murray J., Miller N., Minx P., Fulton R., Johnson D., Bemis G., Bentley D., Bradshaw H., Bourne S., Cordes M., Du Z., Fulton L., Goela D., Graves T., Hawkins J., Hinds K., Kemp K., Latreille P., Layman D., Ozersky P., Rohlfing T., Scheet P., Walker C., Wamsley A., Wohldmann P., Pepin K., Nelson J., Korf I., Bedell J.A., Hillier L.W., Mardis E., Waterston R., Wilson R., Emanuel B.S., Shaikh T., Kurahashi H., Saitta S., Budarf M.L., McDermid H.E., Johnson A., Wong A.C.C., Morrow B.E., Edelmann L., Kim U.J., Shizuya H., Simon M.I., Dumanski J.P., Peyrard M., Kedra D., Seroussi E., Fransson I., Tapia I., Bruder C.E., O'Brien K.P., Wilkinson P., Bodenteich A., Hartman K., Hu X., Khan A.S., Lane L., Tilahun Y., Wright H. Nature 402:489-495(1999) [PubMed: 10591208] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"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]. Tissue: Eye, Lung and Placenta.
[4]	Lubec G., Afjehi-Sadat L., Chen W.-Q., Sun Y. Submitted (DEC-2008) to UniProtKB Cited for: PROTEIN SEQUENCE OF 19-35; 100-119 AND 145-158, MASS SPECTROMETRY. Tissue: Brain, Cajal-Retzius cell and Fetal brain cortex.
[5]	"Identification of an essential cysteine residue in pyridoxal phosphatase from human erythrocytes." Gao G.-J., Fonda M.L. J. Biol. Chem. 269:8234-8239(1994) [PubMed: 8132548] [Abstract] Cited for: PROTEIN SEQUENCE OF 19-30 AND 145-158, ENZYME ACTIVITY.
[6]	Colinge J., Superti-Furga G., Bennett K.L. Submitted (OCT-2008) to UniProtKB Cited for: IDENTIFICATION [LARGE SCALE ANALYSIS], MASS SPECTROMETRY.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

AY125047 mRNA. Translation: AAM94358.1.
Z83844 Genomic DNA. Translation: CAB63038.1.
BC000320 mRNA. Translation: AAH00320.1.
BC009756 mRNA. Translation: AAH09756.2.
BC064922 mRNA. Translation: AAH64922.1.

IPI

IPI00025340.

RefSeq

NP_064711.1.

UniGene

Hs.632762

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2CFR	X-ray	2.40	A	1-296	[»]
2CFS	X-ray	2.40	A	1-296	[»]
2CFT	X-ray	1.80	A	1-296	[»]
2OYC	X-ray	1.72	A	2-296	[»]
2P27	X-ray	1.90	A	2-296	[»]
2P69	X-ray	2.25	A	2-296	[»]

ModBase

Search...

2-D gel databases

REPRODUCTION-2DPAGE

IPI00025340.

Proteomic databases

PeptideAtlas

Q96GD0.

PRIDE

Q96GD0.

Genome annotation databases

Ensembl

ENSG00000221912. Homo sapiens. [Contig view]

GeneID

57026.

KEGG

hsa:57026.

Organism-specific databases

GeneCards

GC22P036379.

H-InvDB

HIX0012724.

HGNC

HGNC:30259. PDXP.

HPA

HPA001099.

MIM

609246. gene.

PharmGKB

PA134882132.

GenAtlas

Search...

Phylogenomic databases

HOVERGEN

Q96GD0.

OMA

Q96GD0. WNGERAV.

Enzyme and pathway databases

BRENDA

3.1.3.74. 247.

Gene expression databases

ArrayExpress

Q96GD0.

Bgee

Q96GD0.

CleanEx

HS_PDXP.

Family and domain databases

InterPro

IPR005834. Dehalogen-like_hydro.
IPR006357. HAD-SF_hydro_IIA.
IPR006349. PGP_euk.
[Graphical view]

Pfam

PF00702. Hydrolase. 1 hit.
[Graphical view]

TIGRFAMs

TIGR01460. HAD-SF-IIA. 1 hit.
TIGR01452. PGP_euk. 1 hit.

ProtoNet

Search...

Other Resources

DrugBank

DB00147. Pyridoxal.
DB00114. Pyridoxal Phosphate.
DB00165. Pyridoxine.

NextBio

62777.

SOURCE

Search...

Entry information

Entry name

PLPP_HUMAN

Accession

Primary (citable) accession number: Q96GD0
Secondary accession number(s): Q9UGY2

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 1, 2004
Last sequence update:	March 1, 2004
Last modified:	June 16, 2009
This is version 63 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)