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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROTEIN O-MANNOSE BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE FORM II
 
Authors :  N. Kuwabara, T. Senda, R. Kato
Date :  15 Jun 16  (Deposition) - 10 Aug 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.49
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Glycosyltransferase, O-Mannosylation, Alpha-Dystroglycan, Transferase, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Kuwabara, H. Manya, T. Yamada, H. Tateno, M. Kanagawa, K. Kobayashi K. Akasaka-Manya, Y. Hirose, M. Mizuno, M. Ikeguchi, T. Toda, J. Hirabayashi, T. Senda, T. Endo, R. Kato
Carbohydrate-Binding Domain Of The Pomgnt1 Stem Region Modulates O-Mannosylation Sites Of Alpha-Dystroglycan
Proc. Natl. Acad. Sci. Usa V. 113 9280 2016
PubMed-ID: 27493216  |  Reference-DOI: 10.1073/PNAS.1525545113

(-) Compounds

Molecule 1 - PROTEIN O-LINKED-MANNOSE BETA-1,2-N- ACETYLGLUCOSAMINYLTRANSFERASE 1
    Chains: A, B, C
    EC Number: 2.4.1.-
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK-293T
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 92-660
    Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5GGF)

(-) Sites  (0, 0)

(no "Site" information available for 5GGF)

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1A:254 -A:281
2A:269 -A:279
3A:421 -A:490
4A:562 -A:596
5B:269 -B:279
6B:421 -B:490
7B:562 -B:596
8C:254 -C:281
9C:269 -C:279
10C:421 -C:490
11C:562 -C:596

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Gly A:218 -Pro A:219
2Ser A:362 -Ile A:363
3Val A:626 -Pro A:627
4Gly B:218 -Pro B:219
5Glu B:250 -Glu B:251
6Ser B:362 -Ile B:363
7Val B:626 -Pro B:627
8Gly C:218 -Pro C:219
9Ser C:362 -Ile C:363
10Val C:626 -Pro C:627

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GGF)

(-) Sequences/Alignments

Asymmetric 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:535
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeee..eeeeee.......eeeeeee......eeeeeee.....hhhhhhhhhhhh.....eeeeeee.......hhhhhhhhhhh............eeeeeee....eeeeeee...........eeeeeeee..hhhhhh......hhhhhhhhhhh....hhhhhh.......................eeeee..hhhhhhhhhhhhhh....hhh.eeeeee..hhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhh....eeeeee..eee..hhhhhhhhhhhhhhhh..eeeee................eeee.......eeeehhhhhhhhhhhh.......hhhhhhhhhhhhh..eeeee....eee................hhhhhhhhhhhhhhhhhhhhhee........hhhhh......eeeeeeee.....hhhhhhhhhhh.........ee..eeeeee..eeeeeeeee.hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggf A  97 RVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSAEEAECHWADTELNRRRRRFCSKVEGYGSVCSCKDPTPIEFSPDPLPDNKVLNVPVAVIAGNRPNYLYRMLRSLLSAQGVSPQMITVFIDGYYEEPMDVVALFGLRGIQHTPISIKNARVSQHYKASLTATFNLFPEAKFAVVLEEDLDIAVDFFSFLSQSIHLLEEDDSLYCISAWNDQGYEHTAEDPALLYRVETMPGLGWVLRRSLYKEELEPKWPTPEKLWDWDMWMRMPEQRRGRECIIPDVSRSYHFGIKHKFNTVPGVQLRNVDSLKKEAYEVEVHRLLSEAEVLDHSKNPCEDSFLPDTEGHTYVAFIRMEKDDDFTTWTQLAKCLHIWDLDVRGNHRGLWRLFRKKNHFLVVGVPASPYSVKKPPSVTPIFLEP 646
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496      |521       531       541       551       561       571       581       591       601       611       621       631       641     
                                                                                                                                                                                                                                                                                                                                                                                                                                                503|                                                                                                                               
                                                                                                                                                                                                                                                                                                                                                                                                                                                 519                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:536
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeee..eeeeee.......eeeeeee......eeeeeee.....hhhhhhhhhhh......eeeeeee.......hhhhhhhhhhh............eeeeeee....eeeeeee...........eeeeeeee.............hhhhhhhhhhhh....hhhhhh.......................eeeee..hhhhhhhhhhhhhh....hhh.eeeee...hhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeee..eee..hhhhhhhhhhhhhhhh..eeeee................eeee.......eeeehhhhhhhhhhhh.......hhhhhhhhhhhhh..eeeee....eee.................hhhhhhhhhhhhhhhhhhhh......................eeeeeee.....hhhhhhhhhhh.........ee..eeee......eeeeeee.hhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggf B  97 RVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSAEEAECHWADTELNRRRRRFCSKVEGYGSVCSCKDPTPIEFSPDPLPDNKVLNVPVAVIAGNRPNYLYRMLRSLLSAQGVSPQMITVFIDGYYEEPMDVVALFGLRGIQHTPISIKNARVSQHYKASLTATFNLFPEAKFAVVLEEDLDIAVDFFSFLSQSIHLLEEDDSLYCISAWNDQGYEHTAEDPALLYRVETMPGLGWVLRRSLYKEELEPKWPTPEKLWDWDMWMRMPEQRRGRECIIPDVSRSYHFGIKHKFNTVPGVQLRNVDSLKKEAYEVEVHRLLSEAEVLDHSKNPCEDSFLPDTEGHTYVAFIRMEKDDDFTTWTQLAKCLHIWDLDVRGNHRGLWRLFRKKNHFLVVGVPASPYSVKKPPSVTPIFLEPP 647
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496      |521       531       541       551       561       571       581       591       601       611       621       631       641      
                                                                                                                                                                                                                                                                                                                                                                                                                                                503|                                                                                                                                
                                                                                                                                                                                                                                                                                                                                                                                                                                                 519                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:536
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeee..eeeeee.......eeeeeee......eeeeeee.....hhhhhhhhhhhh.....eeeeeee.......hhhhhhhhhhh............eeeeeee....eeeeeee...........eeeeeeee..hhhhhh......hhhhhhhhhhh....hhhhhh.......................eeeee..hhhhhhhhhhhhhh....hhh.eeeee...hhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeee..eee..hhhhhhhhhhhhhhhh..eeeee................eeee.......eeeehhhhhhhhhhhh.......hhhhhhhhhhhhh..eeeee....eee................hhhhhhhhhhhhhhhhhhhhhee........hhhhh......eeeeeeee.....hhhhhhhhhhh.........ee..eeeeee..eeeeeeeee...hhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggf C  97 RVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSAEEAECHWADTELNRRRRRFCSKVEGYGSVCSCKDPTPIEFSPDPLPDNKVLNVPVAVIAGNRPNYLYRMLRSLLSAQGVSPQMITVFIDGYYEEPMDVVALFGLRGIQHTPISIKNARVSQHYKASLTATFNLFPEAKFAVVLEEDLDIAVDFFSFLSQSIHLLEEDDSLYCISAWNDQGYEHTAEDPALLYRVETMPGLGWVLRRSLYKEELEPKWPTPEKLWDWDMWMRMPEQRRGRECIIPDVSRSYHFGIKHKFNTVPGVQLRNVDSLKKEAYEVEVHRLLSEAEVLDHSKNPCEDSFLPDTEGHTYVAFIRMEKDDDFTTWTQLAKCLHIWDLDVRGNHRGLWRLFRKKNHFLVVGVPASPYSVKKPPSVTPIFLEPP 647
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496      |521       531       541       551       561       571       581       591       601       611       621       631       641      
                                                                                                                                                                                                                                                                                                                                                                                                                                                503|                                                                                                                                
                                                                                                                                                                                                                                                                                                                                                                                                                                                 519
   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 5GGF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu B:250 - Glu B:251   [ RasMol ]  
    Gly A:218 - Pro A:219   [ RasMol ]  
    Gly B:218 - Pro B:219   [ RasMol ]  
    Gly C:218 - Pro C:219   [ RasMol ]  
    Ser A:362 - Ile A:363   [ RasMol ]  
    Ser B:362 - Ile B:363   [ RasMol ]  
    Ser C:362 - Ile C:363   [ RasMol ]  
    Val A:626 - Pro A:627   [ RasMol ]  
    Val B:626 - Pro B:627   [ RasMol ]  
    Val C:626 - Pro C:627   [ RasMol ]  
 
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 Related Entries

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        PMGT1_HUMAN | Q8WZA1: 5ggg 5ggi 5ggj 5ggk 5ggl 5ggn 5ggo 5ggp

(-) Related Entries Specified in the PDB File

5ggg 5ggi 5ggj 5ggk 5ggl 5ggn 5ggo 5ggp