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(-) Description

Title :  STRUCTURE OF MOUSE GALACTOCEREBROSIDASE WITH 4NBDG: ENZYME-SUBSTRATE COMPLEX
 
Authors :  C. H. Hill, S. C. Graham, R. J. Read, J. E. Deane
Date :  21 Oct 13  (Deposition) - 11 Dec 13  (Release) - 08 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.09
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Krabbe Disease, Glycosyl Hydrolase, 4-Nitrophenyl-Beta-D- Galactopyranoside, Lysosomal Storage Disease, Enzyme- Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. H. Hill, S. C. Graham, R. J. Read, J. E. Deane
Structural Snapshots Illustrate The Catalytic Cycle Of Beta-Galactocerebrosidase, The Defective Enzyme In Krabbe Disease
Proc. Natl. Acad. Sci. Usa V. 110 20479 2013
PubMed-ID: 24297913  |  Reference-DOI: 10.1073/PNAS.1311990110

(-) Compounds

Molecule 1 - GALACTOCEREBROSIDASE
    Chains: A
    EC Number: 3.2.1.46
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Plasmid: PSECTAG2B
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 41-684
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Other Details: FRAGMENT CORRESPONDS TO RESIDUES 25-668 BASED ON NUMBERING STARTING AT SECOND UNIPROT INITIATION SITE.
    Synonym: GALCERASE, GALACTOCEREBROSIDE BETA-GALACTOSIDASE, GALACTOSYLCERAMIDASE, GALACTOSYLCERAMIDE BETA-GALACTOSIDASE, BETA-GALACTOCEREBROSIDASE, GALC

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
11471Ligand/Ion1-O-[P-NITROPHENYL]-BETA-D-GALACTOPYRANOSE
2CA1Ligand/IonCALCIUM ION
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:48 , THR A:92 , THR A:93 , TRP A:135 , ASN A:181 , GLU A:182 , GLU A:258 , SER A:261 , TYR A:303 , ARG A:380 , ARG A:589 , THR A:599 , HOH A:2270 , HOH A:2271BINDING SITE FOR RESIDUE 147 A1001
2AC2SOFTWAREASP A:477 , ASN A:479 , PHE A:511 , ASP A:660 , HOH A:2209BINDING SITE FOR RESIDUE CA A1669
3AC3SOFTWAREILE A:281 , ASN A:284 , HOH A:2272BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1284 THROUGH NAG A1285 BOUND TO ASN A 284
4AC4SOFTWAREASP A:359 , LEU A:361 , ASN A:363BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1363 THROUGH NAG A1364 BOUND TO ASN A 363
5AC5SOFTWARELYS A:350 , TYR A:385 , ASN A:387BINDING SITE FOR MONO-SACCHARIDE NAG A1387 BOUND TO ASN A 387
6AC6SOFTWAREASN A:542 , LYS A:620 , GLY A:621 , ALA A:667 , ARG A:668BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1542 THROUGH NAG A1543 BOUND TO ASN A 542

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:271 -A:378

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Gly A:48 -Gly A:49
2Glu A:60 -Pro A:61
3Ala A:209 -Ser A:210
4Glu A:215 -Pro A:216
5Trp A:291 -Asn A:292
6Arg A:380 -Pro A:381
7Tyr A:641 -Pro A:642

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CCC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CCC)

(-) Exons   (0, 0)

(no "Exon" information available for 4CCC)

(-) 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:640
 aligned with GALC_MOUSE | P54818 from UniProtKB/Swiss-Prot  Length:684

    Alignment length:644
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680    
           GALC_MOUSE    41 GAYVLDDSDGLGREFDGIGAVSGGGATSRLLVNYPEPYRSEILDYLFKPNFGASLHILKVEIGGDGQTTDGTEPSHMHYELDENYFRGYEWWLMKEAKKRNPDIILMGLPWSFPGWLGKGFSWPYVNLQLTAYYVVRWILGAKHYHDLDIDYIGIWNERPFDANYIKELRKMLDYQGLQRVRIIASDNLWEPISSSLLLDQELWKVVDVIGAHYPGTYTVWNAKMSGKKLWSSEDFSTINSNVGAGCWSRILNQNYINGNMTSTIAWNLVASYYEELPYGRSGLMTAQEPWSGHYVVASPIWVSAHTTQFTQPGWYYLKTVGHLEKGGSYVALTDGLGNLTIIIETMSHQHSMCIRPYLPYYNVSHQLATFTLKGSLREIQELQVWYTKLGTPQQRLHFKQLDTLWLLDGSGSFTLELEEDEIFTLTTLTTGRKGSYPPPPSSKPFPTNYKDDFNVEYPLFSEAPNFADQTGVFEYYMNNEDREHRFTLRQVLNQRPITWAADASSTISVIGDHHWTNMTVQCDVYIETPRSGGVFIAGRVNKGGILIRSATGVFFWIFANGSYRVTADLGGWITYASGHADVTAKRWYTLTLGIKGYFAFGMLNGTILWKNVRVKYPGHGWAAIGTHTFEFAQFDNFRVEAAR 684
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeee..eeeeee..............hhhhhhhhhhhh........eeeeee..........................hhhhhhhhhhhhh...eeeeee...hhhhhh.......hhhhhhhhhhhhhhhhhhhhh....ee........hhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhhh.eeeee......hhhhhhhh.eeeeeeee....hhhhhhhhhhhhhhhhhhhh..eeeee..ee.............ee...........hhhhhhhhhhhh......eee...ee.....eeeeee.....eeeeee..hhhhh..............eeeeeee.hhhh...eeeeeeee..----.eeeeeeeeee......eeeeee...eeeeee.....................eeee...............eeee..eeeee........eeeee...............eeeee......eeeeeeeeee......eeeeeeee..hhhhhhh.eeeeeeee...eeeeeee.....eeeeee.......eeeeeeeee..eeeeee..eeeeeeee.......eeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ccc A  25 GAYVLDDSDGLGREFDGIGAVSGGGATSRLLVNYPEPYRSEILDYLFKPNFGASLHILKVEIGGDGQTTDGTEPSHMHYELDENYFRGYEWWLMKEAKKRNPDIILMGLPWSFPGWLGKGFSWPYVNLQLTAYYVVRWILGAKHYHDLDIDYIGIWNERPFDANYIKELRKMLDYQGLQRVRIIASDNLWEPISSSLLLDQELWKVVDVIGAHYPGTYTVWNAKMSGKKLWSSEDFSTINSNVGAGCWSRILNQNYINGNMTSTIAWNLVASYYEELPYGRSGLMTAQEPWSGHYVVASPIWVSAHTTQFTQPGWYYLKTVGHLEKGGSYVALTDGLGNLTIIIETMSHQHSMCIRPYLPYYNVSHQLATFTLKGSLREIQELQVWYTKLG----RLHFKQLDTLWLLDGSGSFTLELEEDEIFTLTTLTTGRKGSYPPPPSSKPFPTNYKDDFNVEYPLFSEAPNFADQTGVFEYYMNNEDREHRFTLRQVLNQRPITWAADASSTISVIGDHHWTNMTVQCDVYIETPRSGGVFIAGRVNKGGILIRSATGVFFWIFANGSYRVTADLGGWITYASGHADVTAKRWYTLTLGIKGYFAFGMLNGTILWKNVRVKYPGHGWAAIGTHTFEFAQFDNFRVEAAR 668
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414|    | 424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664    
                                                                                                                                                                                                                                                                                                                                                                                                                                415  420
   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  (0, 0)

(no "SCOP Domain" information available for 4CCC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GALC_MOUSE | P54818)
molecular function
    GO:0004336    galactosylceramidase activity    Catalysis of the reaction: D-galactosyl-N-acylsphingosine + H2O = D-galactose + N-acylsphingosine.
    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.
biological process
    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:0006683    galactosylceramide catabolic process    The chemical reactions and pathways resulting in the breakdown of galactosylceramides, any compound formed by the replacement of the glycosidic hydroxyl group of a cyclic form of galactose by a ceramide group.
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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.
    GO:0006665    sphingolipid metabolic process    The chemical reactions and pathways involving sphingolipids, any of a class of lipids containing the long-chain amine diol sphingosine or a closely related base (a sphingoid).
cellular component
    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.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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  3.2.1.46
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 Related Entries

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

UniProtKB/Swiss-Prot
        GALC_MOUSE | P54818: 3zr5 3zr6 4ccd 4cce 4ufh 4ufi 4ufj 4ufk 4ufl 4ufm 5n8k 5nxb

(-) Related Entries Specified in the PDB File

4ccd STRUCTURE OF MOUSE GALACTOCEREBROSIDASE WITH D-GALACTAL: ENZYME-INTERMEDIATE COMPLEX
4cce STRUCTURE OF MOUSE GALACTOCEREBROSIDASE WITH GALACTOSE: ENZYME-PRODUCT COMPLEX