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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 GLCNAC-BETA1,2-MAN-PEPTIDE
 
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 :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (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 92-250
    Gene: POMGNT1, MGAT1.2, UNQ746/PRO1475
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 10-MER PEPTIDE FROM DYSTROGLYCAN
    Chains: C, D
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DYSTROPHIN-ASSOCIATED GLYCOPROTEIN 1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1MAN2Ligand/IonALPHA-D-MANNOSE
2NA5Ligand/IonSODIUM ION
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE
2NA-1Ligand/IonSODIUM ION
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE
2NA-1Ligand/IonSODIUM ION
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:207 , SER A:232 , LEU B:231 , MAN C:101binding site for residue NA A 301
2AC2SOFTWARESER A:106 , ARG A:107 , GLY A:235 , PRO A:237 , HOH A:514binding site for residue NA A 302
3AC3SOFTWAREHIS B:155 , HIS B:184 , LYS B:186binding site for residue NA B 301
4AC4SOFTWARELEU A:231 , ARG B:207 , SER B:232 , MAN D:101binding site for residue NA B 302
5AC5SOFTWAREALA B:168 , ARG B:171binding site for residue NA B 303
6AC6SOFTWAREARG A:129 , TYR A:152 , ASP A:179 , GLU A:180 , ARG A:207 , TRP A:234 , NA A:301 , LEU B:231 , HOH B:438 , THR C:4 , HOH C:201 , HOH C:204binding site for Poly-Saccharide residues MAN C 101 through NAG C 102 bound to THR C 4
7AC7SOFTWARELEU A:231 , ARG B:129 , TYR B:152 , ASP B:179 , GLU B:180 , ARG B:207 , TRP B:234 , NA B:302 , THR D:4 , HOH D:207 , HOH D:208 , HOH D:212 , HOH D:213 , HOH D:214 , HOH D:216 , HOH D:220binding site for Poly-Saccharide residues MAN D 101 through NAG D 102 bound to THR D 4

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly B:218 -Pro B:219
2Pro C:5 -Val C:6
3Pro D:5 -Val D:6

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GGP)

(-) 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:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee....eeeee..eeeeee.......eeeeeee......eeeeeee.....hhhhhhhhhhhh.....eeeeeee.......hhhhhhhhhhh...hhhhh....eeeeeee....eeeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ggp A  98 VLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLS 247
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247


Chain B from PDB  Type:PROTEIN  Length:150
                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee....eeeee..eeeeee.......eeeeeee......eeeeeee.....hhhhhhhhhhhh.....eeeeeee.......hhhhhhhhhhh............eeeeeee....eeeeeee...........eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ggp B  98 VLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLS 247
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247


Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5ggp C   2 TPTPV   6


Chain D from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5ggp D   2 TPTPVTAIG  10
   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 5GGP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (74, 78)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DAG1_HUMAN | Q14118: 1eg4 2mk7 5llk
        PMGT1_HUMAN | Q8WZA1: 5ggf 5ggg 5ggi 5ggj 5ggk 5ggl 5ggn 5ggo

(-) Related Entries Specified in the PDB File

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