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(-) Description

Title :  MOUSE GALACTOCEREBROSIDASE IN COMPLEX WITH SAPOSIN A
 
Authors :  S. C. Graham, C. H. Hill, J. E. Deane
Date :  09 May 17  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Krabbe Disease, Galactocerebroside, Galactosylceramide, Galc, Sapa, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. H. Hill, G. M. Cook, S. J. Spratley, S. C. Graham, J. E. Deane
The Mechanism Of Sphingolipid Processing Revealed By A Galc-Sapa Complex Structure
Biorxiv 2017
PubMed: search  |  Reference-DOI: 10.1101/112029

(-) Compounds

Molecule 1 - GALACTOCEREBROSIDASE
    Chains: A, B
    EC Number: 3.2.1.46
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Plasmid: PSECTAG2B-MGALC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: GALC
    Organism Common: 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
 
Molecule 2 - PROSAPOSIN
    Chains: C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Taxid: 562
    Expression System Variant: ORIGAMI
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 59-143
    Gene: PSAP, SGP1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: SULFATED GLYCOPROTEIN 1,SGP-1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3NAG14Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:477 , ASN A:479 , PHE A:511 , ASP A:660binding site for residue CA A 709
02AC2SOFTWAREASP B:477 , ASN B:479 , PHE B:511 , ASP B:660binding site for residue CA B 709
03AC3SOFTWAREARG A:37 , ILE A:281 , ASN A:284binding site for Poly-Saccharide residues NAG A 701 through NAG A 702 bound to ASN A 284
04AC4SOFTWAREASP A:359 , LEU A:361 , ASN A:363binding site for Poly-Saccharide residues NAG A 703 through NAG A 704 bound to ASN A 363
05AC5SOFTWARELYS A:350 , TYR A:385 , ASN A:387binding site for Mono-Saccharide NAG A 705 bound to ASN A 387
06AC6SOFTWARETHR A:541 , ASN A:542 , LYS A:620 , ALA A:667 , ARG A:668binding site for Poly-Saccharide residues NAG A 706 through BMA A 708 bound to ASN A 542
07AC7SOFTWAREARG B:37 , ILE B:281 , ASN B:284binding site for Poly-Saccharide residues NAG B 701 through NAG B 702 bound to ASN B 284
08AC8SOFTWAREASP B:359 , LEU B:361 , ASN B:363binding site for Poly-Saccharide residues NAG B 703 through NAG B 704 bound to ASN B 363
09AC9SOFTWARELYS B:350 , TYR B:385 , ASN B:387 , SER B:389binding site for Mono-Saccharide NAG B 705 bound to ASN B 387
10AD1SOFTWARETHR B:541 , ASN B:542 , LYS B:620 , ALA B:667 , ARG B:668binding site for Poly-Saccharide residues NAG B 706 through BMA B 708 bound to ASN B 542

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:271 -A:378
2B:271 -B:378
3C:4 -C:79
4C:7 -C:73
5C:35 -C:47
6D:4 -D:79
7D:7 -D:73
8D:35 -D:47

(-) Cis Peptide Bonds  (14, 14)

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
8Gly B:48 -Gly B:49
9Glu B:60 -Pro B:61
10Ala B:209 -Ser B:210
11Glu B:215 -Pro B:216
12Trp B:291 -Asn B:292
13Arg B:380 -Pro B:381
14Tyr B:641 -Pro B:642

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5NXB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5NXB)

(-) Exons   (0, 0)

(no "Exon" information available for 5NXB)

(-) 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:644
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               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....hhhhhhhhhhhhhhhhhhhheeeeeee...............................hhhhhhhhhhh......eee...ee.....eeeeee.....eeeeee..hhhhh..............eeeeeee.hhhh...eeeeeeee..hhhhheeeeeeeeee......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
                 5nxb A  25 GAYVLDDSDGLGREFDGIGAVSGGGATSRLLVNYPEPYRSEILDYLFKPNFGASLHILKVEIGGDGQTTDGTEPSHMHYELDENYFRGYEWWLMKEAKKRNPDIILMGLPWSFPGWLGKGFSWPYVNLQLTAYYVVRWILGAKHYHDLDIDYIGIWNERPFDANYIKELRKMLDYQGLQRVRIIASDNLWEPISSSLLLDQELWKVVDVIGAHYPGTYTVWNAKMSGKKLWSSEDFSTINSNVGAGCWSRILNQNYINGNMTSTIAWNLVASYYEELPYGRSGLMTAQEPWSGHYVVASPIWVSAHTTQFTQPGWYYLKTVGHLEKGGSYVALTDGLGNLTIIIETMSHQHSMCIRPYLPYYNVSHQLATFTLKGSLREIQELQVWYTKLGTPQQRLHFKQLDTLWLLDGSGSFTLELEEDEIFTLTTLTTGRKGSYPPPPSSKPFPTNYKDDFNVEYPLFSEAPNFADQTGVFEYYMNNEDREHRFTLRQVLNQRPITWAADASSTISVIGDHHWTNMTVQCDVYIETPRSGGVFIAGRVNKGGILIRSATGVFFWIFANGSYRVTADLGGWITYASGHADVTAKRWYTLTLGIKGYFAFGMLNGTILWKNVRVKYPGHGWAAIGTHTFEFAQFDNFRVEAAR 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    


Chain B from PDB  Type:PROTEIN  Length:644
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               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....hhhhhhhhhhhhhhhhhhhheeeeeee...............................hhhhhhhhhhh......eee...ee.....eeeeee.....eeeeee..hhhhh..............eeeeeee.hhhhhh.eeeeeeee..hhhhheeeeeeeeee......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
                 5nxb B  25 GAYVLDDSDGLGREFDGIGAVSGGGATSRLLVNYPEPYRSEILDYLFKPNFGASLHILKVEIGGDGQTTDGTEPSHMHYELDENYFRGYEWWLMKEAKKRNPDIILMGLPWSFPGWLGKGFSWPYVNLQLTAYYVVRWILGAKHYHDLDIDYIGIWNERPFDANYIKELRKMLDYQGLQRVRIIASDNLWEPISSSLLLDQELWKVVDVIGAHYPGTYTVWNAKMSGKKLWSSEDFSTINSNVGAGCWSRILNQNYINGNMTSTIAWNLVASYYEELPYGRSGLMTAQEPWSGHYVVASPIWVSAHTTQFTQPGWYYLKTVGHLEKGGSYVALTDGLGNLTIIIETMSHQHSMCIRPYLPYYNVSHQLATFTLKGSLREIQELQVWYTKLGTPQQRLHFKQLDTLWLLDGSGSFTLELEEDEIFTLTTLTTGRKGSYPPPPSSKPFPTNYKDDFNVEYPLFSEAPNFADQTGVFEYYMNNEDREHRFTLRQVLNQRPITWAADASSTISVIGDHHWTNMTVQCDVYIETPRSGGVFIAGRVNKGGILIRSATGVFFWIFANGSYRVTADLGGWITYASGHADVTAKRWYTLTLGIKGYFAFGMLNGTILWKNVRVKYPGHGWAAIGTHTFEFAQFDNFRVEAAR 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    


Chain C from PDB  Type:PROTEIN  Length:80
                                                                                                                
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 5nxb C   1 SLPCDICKTVVTEAGNLLKDNATQEEILHYLEKTCEWIHDSSLSASCKEVVDSYLPVILDMIKGEMSNPGEVCSALNLCQ  80
                                    10        20        30        40        50        60        70        80


Chain D from PDB  Type:PROTEIN  Length:80
                                                                                                                
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                 5nxb D   1 SLPCDICKTVVTEAGNLLKDNATQEEILHYLEKTCEWIHDSSLSASCKEVVDSYLPVILDMIKGEMSNPGEVCSALNLCQ  80
                                    10        20        30        40        50        60        70        80
   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 5NXB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5NXB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5NXB)

(-) Gene Ontology  (27, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:209 - Ser A:210   [ RasMol ]  
    Ala B:209 - Ser B:210   [ RasMol ]  
    Arg A:380 - Pro A:381   [ RasMol ]  
    Arg B:380 - Pro B:381   [ RasMol ]  
    Glu A:215 - Pro A:216   [ RasMol ]  
    Glu A:60 - Pro A:61   [ RasMol ]  
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    Glu B:60 - Pro B:61   [ RasMol ]  
    Gly A:48 - Gly A:49   [ RasMol ]  
    Gly B:48 - Gly B:49   [ RasMol ]  
    Trp A:291 - Asn A:292   [ RasMol ]  
    Trp B:291 - Asn B:292   [ RasMol ]  
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    Tyr B:641 - Pro B:642   [ RasMol ]  
 

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  5nxb
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  GALC_MOUSE | P54818
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  SAP_MOUSE | Q61207
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 Related Entries

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

UniProtKB/Swiss-Prot
        GALC_MOUSE | P54818: 3zr5 3zr6 4ccc 4ccd 4cce 4ufh 4ufi 4ufj 4ufk 4ufl 4ufm 5n8k
        SAP_MOUSE | Q61207: 5n8k

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5NXB)