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(-) Description

Title :  CRYSTAL STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN PROTEIN O-MANNOSE BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE IN COMPLEX WITH GALNAC-BETA1,3-GLCNAC-BETA-PNP
 
Authors :  N. Kuwabara, T. Senda, R. Kato
Date :  16 Jun 16  (Deposition) - 10 Aug 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycosyltransferease, O-Mannosylation, Alpha-Dystroglycan, 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
    EC Number: 2.4.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 97-250
    Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2LEC2Ligand/IonN-[(2S,3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-2-(4-NITROPHENOXY)OXAN-3-YL]ETHANAMIDE
3NGA2Ligand/IonN-ACETYL-D-GALACTOSAMINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2LEC1Ligand/IonN-[(2S,3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-2-(4-NITROPHENOXY)OXAN-3-YL]ETHANAMIDE
3NGA1Ligand/IonN-ACETYL-D-GALACTOSAMINE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2LEC1Ligand/IonN-[(2S,3R,4R,5S,6R)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-2-(4-NITROPHENOXY)OXAN-3-YL]ETHANAMIDE
3NGA1Ligand/IonN-ACETYL-D-GALACTOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:109 , TYR A:111 , GLU A:121 , HOH A:475 , ARG B:147 , HOH B:486binding site for residue EDO B 303
2AC2SOFTWAREARG A:125 , GLU A:126 , ARG A:129 , ASP A:179 , GLU A:180 , ARG A:207 , HOH A:433 , HOH A:479 , HOH A:486 , HOH A:487binding site for Poly-Saccharide residues LEC A 301 through NGA A 302
3AC3SOFTWAREARG B:129 , TYR B:152 , ASP B:179 , GLU B:180 , PHE B:183 , TRP B:206 , ARG B:207 , HOH B:420 , HOH B:422 , HOH B:423binding site for Poly-Saccharide residues LEC B 301 through NGA B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GGO)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:218 -Pro A:219
2Gly B:218 -Pro B:219

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GGO)

(-) 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:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeee..eeeeee.......eeeeeee......eeeeeee.....hhhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhh...hhhhh....eeeeeee....eeeeeee...........eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggo A  97 RVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSA 249
                                   106       116       126       136       146       156       166       176       186       196       206       216       226       236       246   


Chain B from PDB  Type:PROTEIN  Length:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eeeee..eeeeee.......eeeeeee......eeeeeee.....hhhhhhhhhhhhh....eeeeeee.......hhhhhhhhhhh...hhhhh....eeeeeee....eeeeeee...........eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggo B  98 VLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSS 248
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247
   Legend:   → Mismatch (orange background)
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  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 5GGO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

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 Related Entries

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UniProtKB/Swiss-Prot
        PMGT1_HUMAN | Q8WZA1: 5ggf 5ggg 5ggi 5ggj 5ggk 5ggl 5ggn 5ggp

(-) Related Entries Specified in the PDB File

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