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(-) Description

Title :  PHARMACOLOGICAL CHAPERONES FOR HUMAN ALPHA-N-ACETYLGALACTOSAMINIDASE
 
Authors :  N. E. Clark, S. C. Garman
Date :  09 Feb 12  (Deposition) - 10 Oct 12  (Release) - 21 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta/Alpha)8 Barrel, Glycosidase, Carbohydrate-Binding Protein, Glycoprotein, Lysosome, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. E. Clark, M. C. Metcalf, D. Best, G. W. Fleet, S. C. Garman
Pharmacological Chaperones For Human Alpha-N-Acetylgalactosaminidase
Proc. Natl. Acad. Sci. Usa V. 109 17400 2012
PubMed-ID: 23045655  |  Reference-DOI: 10.1073/PNAS.1203924109

(-) Compounds

Molecule 1 - ALPHA-N-ACETYLGALACTOSAMINIDASE
    Chains: A, B
    EC Number: 3.2.1.49
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PIB/V5-HIS-TOPO TA
    Expression System Strain: HI-FIVE
    Expression System Taxid: 7111
    Expression System Vector Type: PLASMID
    Gene: NAGA
    Mutation: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-GALACTOSIDASE B

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (8, 25)

Asymmetric/Biological Unit (8, 25)
No.NameCountTypeFull Name
12PE2Ligand/IonNONAETHYLENE GLYCOL
2BGC1Ligand/IonBETA-D-GLUCOSE
3BMA3Ligand/IonBETA-D-MANNOSE
4CIT1Ligand/IonCITRIC ACID
5FUC1Ligand/IonALPHA-L-FUCOSE
6GLC3Ligand/IonALPHA-D-GLUCOSE
7MAN4Ligand/IonALPHA-D-MANNOSE
8NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:124 , NAG A:502 , HOH A:725 , HOH A:997 , HOH A:1029BINDING SITE FOR RESIDUE NAG A 501
02AC2SOFTWARENAG A:501 , BMA A:503 , HOH A:1040BINDING SITE FOR RESIDUE NAG A 502
03AC3SOFTWAREPHE A:159 , NAG A:502 , HOH A:855BINDING SITE FOR RESIDUE BMA A 503
04AC4SOFTWAREASP A:19 , ASN A:20 , ASN A:177 , GLY A:180 , NAG A:505 , HOH A:639 , HOH A:735 , HOH A:825 , HOH A:870BINDING SITE FOR RESIDUE NAG A 504
05AC5SOFTWAREASP A:19 , NAG A:504 , BMA A:506 , MAN A:508 , HOH A:889BINDING SITE FOR RESIDUE NAG A 505
06AC6SOFTWARENAG A:505 , MAN A:507 , MAN A:508 , HOH A:889 , HOH A:1042 , GLN B:64 , ASP B:65BINDING SITE FOR RESIDUE BMA A 506
07AC7SOFTWAREBMA A:506 , HOH A:939BINDING SITE FOR RESIDUE MAN A 507
08AC8SOFTWARENAG A:505 , BMA A:506 , HOH A:769BINDING SITE FOR RESIDUE MAN A 508
09AC9SOFTWAREGLU A:383 , ASN A:385 , HOH A:800BINDING SITE FOR RESIDUE NAG A 509
10BC1SOFTWAREILE A:40 , ASN A:41 , CYS A:42 , ASP A:43 , ASP A:94 , LYS A:96 , ARG A:97 , HOH A:684 , HOH A:1034BINDING SITE FOR RESIDUE CIT A 510
11BC2SOFTWARELEU A:323 , ARG A:344 , THR A:345 , ASP A:346 , HOH A:914 , ARG B:37 , GLN B:219BINDING SITE FOR RESIDUE GLC A 511
12BC3SOFTWAREGLU A:264 , ARG A:267 , ASP A:370 , SER A:373 , VAL A:395 , VAL A:396 , HOH A:620 , HOH A:751 , HOH A:1027BINDING SITE FOR RESIDUE GLC A 512
13BC4SOFTWAREASN B:124 , PHE B:159 , SER B:160 , NAG B:502 , FUC B:503BINDING SITE FOR RESIDUE NAG B 501
14BC5SOFTWARENAG B:501BINDING SITE FOR RESIDUE NAG B 502
15BC6SOFTWARENAG B:501BINDING SITE FOR RESIDUE FUC B 503
16BC7SOFTWAREARG A:199 , HOH A:727 , ASP B:19 , ASN B:20 , ASN B:177 , GLY B:180 , NAG B:505 , HOH B:629 , HOH B:659 , HOH B:668 , HOH B:688BINDING SITE FOR RESIDUE NAG B 504
17BC8SOFTWAREARG A:199 , ASP B:19 , GLY B:21 , NAG B:504 , BMA B:506 , MAN B:508BINDING SITE FOR RESIDUE NAG B 505
18BC9SOFTWARENAG B:505 , MAN B:507 , MAN B:508 , HOH B:841BINDING SITE FOR RESIDUE BMA B 506
19CC1SOFTWAREBMA B:506BINDING SITE FOR RESIDUE MAN B 507
20CC2SOFTWARENAG B:505 , BMA B:506BINDING SITE FOR RESIDUE MAN B 508
21CC3SOFTWAREGLU B:383 , ASN B:385BINDING SITE FOR RESIDUE NAG B 509
22CC4SOFTWAREARG A:37 , GLN A:219 , LEU B:323 , ARG B:344 , THR B:345 , ASP B:346 , HOH B:720 , HOH B:921BINDING SITE FOR RESIDUE BGC B 511
23CC5SOFTWAREGLU B:264 , ARG B:267 , ASP B:370 , SER B:373 , VAL B:395 , VAL B:396 , HOH B:649 , HOH B:709 , HOH B:836BINDING SITE FOR RESIDUE GLC B 512

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:38 -A:80
2A:42 -A:49
3A:127 -A:158
4A:187 -A:209
5B:38 -B:80
6B:42 -B:49
7B:127 -B:158
8B:187 -B:209

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro A:197 -Pro A:198
2Pro B:197 -Pro B:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric/Biological Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_000496S160CNAGAB_HUMANDisease (SCHIND)121434532A/BS160C
2UniProtVAR_000497E325KNAGAB_HUMANDisease (SCHIND)121434529A/BE325K
3UniProtVAR_022525R329QNAGAB_HUMANDisease (KANZD)121434533A/BR329Q
4UniProtVAR_000498R329WNAGAB_HUMANDisease (KANZD)121434530A/BR329W
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALPHA_GALACTOSIDASEPS00512 Alpha-galactosidase signature.NAGAB_HUMAN71-86
 		  2A:71-86
B:71-86

(-) Exons   (0, 0)

(no "Exon" information available for 4DO6)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:388
 aligned with NAGAB_HUMAN | P17050 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:388
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397        
          NAGAB_HUMAN    18 LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVNYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKN 405
               SCOP domains d4do6a1 A:18-309 automated matches                                                                                                                                                                                                                                                                  d4do6a2 A:310-405 automated matches                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeehhhhhh.............hhhhhhhhhhhhhhhhhhhhh..eee.....eeee.....eee.......hhhhhhhhhhhh..eeeeeee............hhhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhh....eeeehhhhhh.......hhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhh.......eeeee....eeeeeee.hhh.eeeeeee......eeeee.hhhhh......eeeee.....eeeee.....eeeee....eeeeeeee... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------------------------------------------------------------------C--------------------------------------------------------------------------------------------------------------------------------------------------------------------K---Q---------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W---------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------ALPHA_GALACTOSID------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4do6 A  18 LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKN 405
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397        


Chain B from PDB  Type:PROTEIN  Length:400
 aligned with NAGAB_HUMAN | P17050 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:400
                                                                                                                                                                                                                                                                                                                                                                                                                                   411      
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407   |     -
          NAGAB_HUMAN    18 LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVNYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQ------   -
               SCOP domains d4do6b1 B:18-309 automated matches                                                                                                                                                                                                                                                                  d4do6b2 B:310-417 automated matches                                                                          SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeehhhhhh.............hhhhhhhhhhhhhhhhhhhhh..eee.....eeee.....eee.......hhhhhhhhhhhh..eeeeeee............hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhh....eeee.hhhhhh......hhhhhhhhh.eee.......hhhhhhhhhhhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhh.......eeeee....eeeeeee.hhh.eeeeeee......eeeeehhhhhh......eeeee.....eeeee.....eeeee....eeeeeeeehhhhhhhhh...... Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------------------------------------------------------------------------------------------------------------------C--------------------------------------------------------------------------------------------------------------------------------------------------------------------K---Q---------------------------------------------------------------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W---------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -----------------------------------------------------ALPHA_GALACTOSID------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4do6 B  18 LDNGLLQTPPMGWLAWERFRCNINCDEDPKNCISEQLFMEMADRMAQDGWRDMGYTYLNIDDCWIGGRDASGRLMPDPKRFPHGIPFLADYVHSLGLKLGIYADMGNFTCMGYPGTTLDKVVQDAQTFAEWKVDMLKLDGCFSTPEERAQGYPKMAAALNATGRPIAFSCSWPAYEGGLPPRVQYSLLADICNLWRNYDDIQDSWWSVLSILNWFVEHQDILQPVAGPGHWNDPDMLLIGNFGLSLEQSRAQMALWTVLAAPLLMSTDLRTISAQNMDILQNPLMIKINQDPLGIQGRRIHKEKSLIEVYMRPLSNKASALVFFSCRTDMPYRYHSSLGQLNFTGSVIYEAQDVYSGDIISGLRDETNFTVIINPSGVVMWYLYPIKNLEMSQQHHHHHH 417
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DO6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DO6)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (NAGAB_HUMAN | P17050)
molecular function
    GO:0008456    alpha-N-acetylgalactosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-galactosamine residues in N-acetyl-alpha-D-galactosaminides.
    GO:0004557    alpha-galactosidase activity    Catalysis of the hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0016052    carbohydrate catabolic process    The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0019377    glycolipid catabolic process    The chemical reactions and pathways resulting in the breakdown of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide).
    GO:0016139    glycoside catabolic process    The chemical reactions and pathways resulting in the breakdown of glycosides, compounds in which a glycosyl group is substituted into a hydroxyl, thiol or selenol group in another compound.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NAGAB_HUMAN | P17050: 3h53 3h54 3h55 3igu 4do4 4do5

(-) Related Entries Specified in the PDB File

3h53 COMPLEX WITH GLYCEROL
3h54 COMPLEX WITH GALNAC
3h55 COMPLEX WITH GALACTOSE
3igu COVALENT COMPLEX
4do4 COMPLEX WITH DGJNAC
4do5 COMPLEX WITH DGJ