P17050 (NAGAB_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Alpha-N-acetylgalactosaminidase
EC=3.2.1.49

Alternative name(s):
Alpha-galactosidase B

Gene names

Name:

NAGA

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	411 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Removes terminal alpha-N-acetylgalactosamine residues from glycolipids and glycopeptides. Required for the breakdown of glycolipids. Ref.9
Catalytic activity	Cleavage of non-reducing alpha-(1->3)-N-acetylgalactosamine residues from human blood group A and AB mucin glycoproteins, Forssman hapten and blood group A lacto series glycolipids. Ref.12
Subunit structure	Homodimer. Ref.12
Subcellular location	Lysosome.
Involvement in disease	Defects in NAGA are the cause of Schindler disease (SCHIND) [MIM:609241]. Schindler disease is a form of NAGA deficiency characterized by early onset neuroaxonal dystrophy and neurological signs (convulsion during fever, epilepsy, psychomotor retardation and hypotonia). NAGA deficiency is typically classified in three main phenotypes: NAGA deficiency type I (Schindler disease or Schindler disease type I) with severe manifestations; NAGA deficiency type II (Kanzazi disease or Schindler disease type II) which is mild; NAGA deficiency type III (Schindler disease type III) characterized by mild-to-moderate neurologic manifestations. NAGA deficiency results in the increased urinary excretion of glycopeptides and oligosaccharides containing alpha-N-acetylgalactosaminyl moieties. Inheritance is autosomal recessive. Ref.13 Ref.15 Defects in NAGA are the cause of Kanzaki disease (KANZD) [MIM:609242]; also known as NAGA deficiency type II or Schindler disease type II. Kanzaki disease is an autosomal recessive disorder characterized by late onset, angiokeratoma corporis diffusum and mild intellectual impairment. Ref.14 Ref.16
Miscellaneous	Alpha-galactosidase B was first found to be an isoenzyme of alpha-galactosidases, but apparently it differs from alpha-galactosidase A in substrate specificity and is alpha-N-acetylgalactosaminidase.
Sequence similarities	Belongs to the glycosyl hydrolase 27 family.
Sequence caution	The sequence AAA59902.1 differs from that shown. Reason: Frameshift at position 320.

Ontologies

Keywords
Cellular component	Lysosome
Disease	Disease mutation Epilepsy
Domain	Signal
Molecular function	Glycosidase Hydrolase
PTM	Disulfide bond Glycoprotein Phosphoprotein
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological process	glycoside catabolic process Inferred from Biological aspect of Ancestor. Source: RefGenome glycosylceramide catabolic process Inferred from Biological aspect of Ancestor. Source: RefGenome oligosaccharide metabolic process Inferred from Biological aspect of Ancestor. Source: RefGenome
Cellular component	lysosome Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	alpha-N-acetylgalactosaminidase activity Inferred from direct assay Ref.12. Source: UniProtKB alpha-galactosidase activity Inferred from Biological aspect of Ancestor. Source: RefGenome cation binding Inferred from electronic annotation. Source: InterPro protein homodimerization activity Inferred from physical interaction Ref.12. Source: UniProtKB
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Signal peptide

1 – 17

17

Ref.8

Chain

18 – 411

394

Alpha-N-acetylgalactosaminidase

PRO_0000001018

Regions

Region

78 – 79

2

Substrate binding

Sites

Active site

156

1

Nucleophile

Active site

217

1

Proton donor

Binding site

154

1

Substrate

Binding site

188

1

Substrate

Binding site

213

1

Substrate

Binding site

217

1

Substrate

Amino acid modifications

Modified residue

322

1

Phosphoserine Ref.10

Modified residue

332

1

Phosphoserine Ref.10

Glycosylation

124

1

N-linked (GlcNAc...) Ref.12

Glycosylation

177

1

N-linked (GlcNAc...) Ref.11 Ref.12

Glycosylation

201

1

N-linked (GlcNAc...) Ref.11

Glycosylation

359

1

N-linked (GlcNAc...) Potential

Glycosylation

385

1

N-linked (GlcNAc...) Ref.12

Disulfide bond

38 ↔ 80

Ref.12

Disulfide bond

42 ↔ 49

Ref.12

Disulfide bond

127 ↔ 158

Ref.12

Disulfide bond

187 ↔ 209

Ref.12

Natural variations

Natural variant

160

1

S → C in SCHIND; type III. Ref.15

VAR_000496

Natural variant

325

1

E → K in SCHIND; type I and type III. Ref.13 Ref.15

VAR_000497

Natural variant

329

1

R → Q in KANZD. Ref.16

VAR_022525

Natural variant

329

1

R → W in KANZD; loss of activity. Ref.14

VAR_000498

Experimental info

Mutagenesis

201

1

N → Q: Loss of glycosylation site; no effect on enzyme activity and stability. Ref.12

Sequence conflict

24

1

Q → N AA sequence Ref.8

Sequence conflict

165

1

R → A in AAA59902. Ref.2

Sequence conflict

175

1

A → G in AAA59902. Ref.2

Sequence conflict

205

1

L → Q in AAA59902. Ref.2

Secondary structure

1

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411

Helix Strand Turn

Details...

Helix

33 – 36

4

Turn

42 – 44

3

Turn

46 – 48

3

Beta strand

49 – 51

3

Helix

52 – 64

13

Turn

95 – 97

3

Helix

103 – 111

9

Beta strand

119 – 121

3

Helix

135 – 137

3

Helix

138 – 147

10

Beta strand

152 – 156

5

Helix

162 – 166

5

Helix

170 – 178

9

Beta strand

184 – 187

4

Helix

189 – 192

4

Turn

197 – 199

3

Helix

202 – 208

7

Beta strand

210 – 213

4

Helix

222 – 234

13

Helix

236 – 239

4

Turn

240 – 242

3

Beta strand

248 – 250

3

Helix

263 – 275

13

Turn

286 – 288

3

Helix

291 – 297

7

Helix

300 – 306

7

Beta strand

316 – 319

4

Beta strand

323 – 330

8

Beta strand

336 – 342

7

Beta strand

345 – 347

3

Beta strand

349 – 354

6

Beta strand

366 – 371

6

Beta strand

385 – 390

6

Beta strand

396 – 402

7

Sequences

	Sequence		Length	Mass (Da)
	P17050 [UniParc]. Last modified March 1, 1992. Version 2. Checksum: 781A0728C0B29CD9	FASTA	411	46,565
	10 20 30 40 50 60 MLLKTVLLLG HVAQVLMLDN GLLQTPPMGW LAWERFRCNI NCDEDPKNCI SEQLFMEMAD 70 80 90 100 110 120 RMAQDGWRDM GYTYLNIDDC WIGGRDASGR LMPDPKRFPH GIPFLADYVH SLGLKLGIYA 130 140 150 160 170 180 DMGNFTCMGY PGTTLDKVVQ DAQTFAEWKV DMLKLDGCFS TPEERAQGYP KMAAALNATG 190 200 210 220 230 240 RPIAFSCSWP AYEGGLPPRV NYSLLADICN LWRNYDDIQD SWWSVLSILN WFVEHQDILQ 250 260 270 280 290 300 PVAGPGHWND PDMLLIGNFG LSLEQSRAQM ALWTVLAAPL LMSTDLRTIS AQNMDILQNP 310 320 330 340 350 360 LMIKINQDPL GIQGRRIHKE KSLIEVYMRP LSNKASALVF FSCRTDMPYR YHSSLGQLNF 370 380 390 400 410 TGSVIYEAQD VYSGDIISGL RDETNFTVII NPSGVVMWYL YPIKNLEMSQ Q

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Human alpha-N-acetylgalactosaminidase-molecular cloning, nucleotide sequence, and expression of a full-length cDNA. Homology with human alpha-galactosidase A suggests evolution from a common ancestral gene." Wang A.M., Bishop D.F., Desnick R.J. J. Biol. Chem. 265:21859-21866(1990) [PubMed: 2174888] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], PARTIAL PROTEIN SEQUENCE. Tissue: Lung.
[2]	"Structural organization and complete sequence of the human alpha-N-acetylgalactosaminidase gene: homology with the alpha-galactosidase A gene provides evidence for evolution from a common ancestral gene." Wang A.M., Desnick R.J. Genomics 10:133-142(1991) [PubMed: 1646157] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[3]	"Molecular cloning of a full-length cDNA for human alpha-N-acetylgalactosaminidase (alpha-galactosidase B)." Tsuji S., Yamauchi T., Hiraiwa M., Isobe T., Okuyama T., Sakimura K., Takahashi Y., Nishizawa M., Uda Y., Miyatake T. Biochem. Biophys. Res. Commun. 163:1498-1504(1989) [PubMed: 2551294] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Tissue: Placenta.
[4]	"Molecular cloning of two species of cDNAs for human alpha-N-acetylgalactosaminidase and expression in mammalian cells." Yamauchi T., Hiraiwa M., Kobayashi H., Uda Y., Miyatake T., Tsuji S. Biochem. Biophys. Res. Commun. 170:231-237(1990) [PubMed: 2372288] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[5]	"A genome annotation-driven approach to cloning the human ORFeome." Collins J.E., Wright C.L., Edwards C.A., Davis M.P., Grinham J.A., Cole C.G., Goward M.E., Aguado B., Mallya M., Mokrab Y., Huckle E.J., Beare D.M., Dunham I. Genome Biol. 5:R84.1-R84.11(2004) [PubMed: 15461802] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
[6]	"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].
[7]	"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: Placenta.
[8]	"Photolabeling of the alpha-neuraminidase/beta-galactosidase complex from human placenta with a photoreactive neuraminidase inhibitor." Warner T.G., Louie A., Potier M. Biochem. Biophys. Res. Commun. 173:13-19(1990) [PubMed: 2256909] [Abstract] Cited for: PROTEIN SEQUENCE OF 18-37. Tissue: Placenta.
[9]	"Degradation of blood group A glycolipid A-6-2 by normal and mutant human skin fibroblasts." Asfaw B., Schindler D., Ledvinova J., Cerny B., Smid F., Conzelmann E. J. Lipid Res. 39:1768-1780(1998) [PubMed: 9741689] [Abstract] Cited for: FUNCTION.
[10]	"Quantitative phosphoproteome profiling of Wnt3a-mediated signaling network: indicating the involvement of ribonucleoside-diphosphate reductase M2 subunit phosphorylation at residue serine 20 in canonical Wnt signal transduction." Tang L.-Y., Deng N., Wang L.-S., Dai J., Wang Z.-L., Jiang X.-S., Li S.-J., Li L., Sheng Q.-H., Wu D.-Q., Li L., Zeng R. Mol. Cell. Proteomics 6:1952-1967(2007) [PubMed: 17693683] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-322 AND SER-332, MASS SPECTROMETRY. Tissue: Embryonic kidney.
[11]	"Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry." Chen R., Jiang X., Sun D., Han G., Wang F., Ye M., Wang L., Zou H. J. Proteome Res. 8:651-661(2009) [PubMed: 19159218] [Abstract] Cited for: GLYCOSYLATION [LARGE SCALE ANALYSIS] AT ASN-177 AND ASN-201, MASS SPECTROMETRY. Tissue: Liver.
[12]	"The 1.9 A structure of human alpha-N-acetylgalactosaminidase: the molecular basis of Schindler and Kanzaki diseases." Clark N.E., Garman S.C. J. Mol. Biol. 393:435-447(2009) [PubMed: 19683538] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF 18-411 IN COMPLEXES WITH N-ACETYLGALACTOSAMINE AND GALACTOSE, DISULFIDE BONDS, GLYCOSYLATION AT ASN-124; ASN-177 AND ASN-385, SUBUNIT, CATALYTIC ACTIVITY, MUTAGENESIS OF ASN-201.
[13]	"Schindler disease: the molecular lesion in the alpha-N-acetylgalactosaminidase gene that causes an infantile neuroaxonal dystrophy." Wang A.M., Schindler D., Desnick R.J. J. Clin. Invest. 86:1752-1756(1990) [PubMed: 2243144] [Abstract] Cited for: VARIANT SCHIND LYS-325.
[14]	"The molecular lesion in the alpha-N-acetylgalactosaminidase gene that causes angiokeratoma corporis diffusum with glycopeptiduria." Wang A.M., Kanzaki T., Desnick R.J. J. Clin. Invest. 94:839-845(1994) [PubMed: 8040340] [Abstract] Cited for: VARIANT KANZD TRP-329, CHARACTERIZATION OF VARIANT KANZD TRP-329.
[15]	"Human alpha-N-acetylgalactosaminidase (alpha-NAGA) deficiency: new mutations and the paradox between genotype and phenotype." Keulemans J.L.M., Reuser A.J.J., Kroos M.A., Willemsen R., Hermans M.M.P., van den Ouweland A.M.W., de Jong J.G.N., Wevers R.A., Renier W.O., Schindler D., Coll M.J., Chabas A., Sakuraba H., Suzuki Y., van Diggelen O.P. J. Med. Genet. 33:458-464(1996) [PubMed: 8782044] [Abstract] Cited for: VARIANTS SCHIND CYS-160 AND LYS-325.
[16]	"A new case of alpha-N-acetylgalactosaminidase deficiency with angiokeratoma corporis diffusum, with Meniere's syndrome and without mental retardation." Kodama K., Kobayashi H., Abe R., Ohkawara A., Yoshii N., Yotsumoto S., Fukushige T., Nagatsuka Y., Hirabayashi Y., Kanzaki T. Br. J. Dermatol. 144:363-368(2001) [PubMed: 11251574] [Abstract] Cited for: VARIANT KANZD GLN-329.
+	Additional computationally mapped references.

Web resources

GeneReviews

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

M62783 mRNA. Translation: AAA51677.1.
M59199 Genomic DNA. Translation: AAB06718.1.
M29276 mRNA. Translation: AAA59902.1. Frameshift.
M38083 mRNA. Translation: AAA36351.1.
CR456527 mRNA. Translation: CAG30413.1.
Z99716 Genomic DNA. Translation: CAB41237.1.
BC000095 mRNA. Translation: AAH00095.1.

IPI

IPI00414909.

PIR

A33265.
A35485. A36530.

RefSeq

NP_000253.1. NM_000262.2.

UniGene

Hs.75372.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3H53	X-ray	2.01	A/B	18-411	[»]
3H54	X-ray	2.20	A/B	18-411	[»]
3H55	X-ray	1.91	A/B	18-411	[»]
3IGU	X-ray	2.15	A/B	18-411	[»]

ProteinModelPortal

P17050.

SMR

P17050. Positions 18-404.

ModBase

Search...

Protein-protein interaction databases

STRING

P17050.

Protein family/group databases

CAZy

GH27. Glycoside Hydrolase Family 27.

PTM databases

GlycoSuiteDB

P17050.

Polymorphism databases

DMDM

127801.

Proteomic databases

PeptideAtlas

P17050.

PRIDE

P17050.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000396398; ENSP00000379680; ENSG00000198951.
ENST00000402937; ENSP00000384603; ENSG00000198951.
ENST00000403363; ENSP00000385283; ENSG00000198951.

GeneID

4668.

KEGG

hsa:4668.

UCSC

uc003bbw.2. human.

Organism-specific databases

CTD

4668.

GeneCards

GC22M042428.

H-InvDB

HIX0016536.

HGNC

HGNC:7631. NAGA.

HPA

HPA000649.

MIM

104170. gene.
609241. phenotype.
609242. phenotype.

neXtProt

NX_P17050.

Orphanet

3137. Alpha-N-acetylgalactosaminidase deficiency.

PharmGKB

PA31435.

GenAtlas

Search...

Phylogenomic databases

eggNOG

prNOG13405.

GeneTree

ENSGT00390000008751.

HOGENOM

HBG424315.

HOVERGEN

HBG001989.

InParanoid

P17050.

OMA

DEDPKNC.

PhylomeDB

P17050.

Enzyme and pathway databases

BioCyc

MetaCyc:HS01993-MONOMER.

Gene expression databases

ArrayExpress

P17050.

Bgee

P17050.

CleanEx

HS_NAGA.

Genevestigator

P17050.

GermOnline

ENSG00000198951. Homo sapiens.

Family and domain databases

InterPro

IPR013785. Aldolase_TIM.
IPR013780. Glyco_hydro_13_b.
IPR002241. Glyco_hydro_27.
IPR000111. Glyco_hydro_GHD.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]

Gene3D

G3DSA:3.20.20.70. Aldolase_TIM. 1 hit.
G3DSA:2.60.40.1180. Glyco_hydro_13_b. 1 hit.

KO

K01204.

Pfam

PF02065. Melibiase. 1 hit.
[Graphical view]

PRINTS

PR00740. GLHYDRLASE27.

SUPFAM

SSF51445. Glyco_hydro_cat. 1 hit.

PROSITE

PS00512. ALPHA_GALACTOSIDASE. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

NextBio

17986.

SOURCE

Search...

Entry information

Entry name

NAGAB_HUMAN

Accession

Primary (citable) accession number: P17050

Entry history

Integrated into UniProtKB/Swiss-Prot:	August 1, 1990
Last sequence update:	March 1, 1992
Last modified:	January 25, 2012
This is version 127 of the entry and version 2 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.