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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROTEIN O-MANNOSE BETA-1,2-N-ACETYLGLUCOSAMINYLTRANSFERASE IN COMPLEX WITH MN, UDP AND MANNOSYL-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 :  2.60
Chains :  Asym. Unit :  A,B,F,G
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B,F,G  (1x)
Keywords :  Glycosyltransferease, O-Mannosylation, Alpha-Dystroglycan, Transferase, Sugar Binding Protein-Substrate Complex (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: 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
 
Molecule 2 - MANNOSYL-PEPTIDE
    Chains: F, G
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABFG
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  BFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric Unit (5, 8)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2MAN2Ligand/IonALPHA-D-MANNOSE
3MN2Ligand/IonMANGANESE (II) ION
4PO41Ligand/IonPHOSPHATE ION
5UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACE-1Mod. Amino AcidACETYL GROUP
2MAN-1Ligand/IonALPHA-D-MANNOSE
3MN-1Ligand/IonMANGANESE (II) ION
4PO41Ligand/IonPHOSPHATE ION
5UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2MAN2Ligand/IonALPHA-D-MANNOSE
3MN-1Ligand/IonMANGANESE (II) ION
4PO4-1Ligand/IonPHOSPHATE ION
5UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:307 , ALA A:308 , GLY A:309 , ARG A:311 , ASP A:338 , ARG A:367 , VAL A:368 , HIS A:371 , GLU A:393 , GLU A:394 , ASP A:395 , GLY A:505 , LEU A:506 , ASN A:507 , MET A:508 , MN A:702binding site for residue UDP A 701
2AC2SOFTWAREGLU A:393 , ASP A:395 , HIS A:500 , UDP A:701binding site for residue MN A 702
3AC3SOFTWARELEU A:439 , ARG A:531 , HIS A:620binding site for residue PO4 A 703
4AC4SOFTWAREILE B:307 , ALA B:308 , GLY B:309 , ARG B:311 , ASP B:338 , ARG B:367 , VAL B:368 , HIS B:371 , GLU B:393 , GLU B:394 , ASP B:395 , GLY B:505 , LEU B:506 , ASN B:507 , MET B:508 , MN B:702 , MAN G:101 , HOH G:201binding site for residue UDP B 701
5AC5SOFTWAREASP B:395 , HIS B:500 , UDP B:701binding site for residue MN B 702
6AC6SOFTWAREARG B:129 , ASP B:179 , ARG B:207 , TRP B:234 , THR F:4 , VAL F:6binding site for Mono-Saccharide MAN F 101 bound to THR F 4
7AC7SOFTWAREASP B:476 , ARG B:480 , ASN B:507 , PHE B:512 , TRP B:600 , ARG B:605 , UDP B:701 , THR G:4 , HOH G:201binding site for Mono-Saccharide MAN G 101 bound to THR G 4
8AC8SOFTWAREARG A:317 , PHE A:501 , ILE A:503 , HIS A:513 , ALA F:2 , PRO F:3binding site for Di-peptide ACE F 0 and ALA F 1

(-) SS Bonds  (8, 8)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:626 -Pro A:627
2Val B:626 -Pro B:627

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GGI)

(-) 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:394
                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh....hhhhh........................eeeee..hhhhhhhhhhhhh.....hhh.eeeee...hhhhhhhhhhhh.eeee.....hhhhhhhhhhhhhhhhhhhhh....eeeeee..eee..hhhhhhhhhhhhhhhh..eeeee................eeee.......eeeehhhhhhhhhhhh.......hhhhhhhhhhhhh..eeeee....eee........hhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhee........hhhhh......eeeeeeee.....hhhhhhhhhhhh............eeeeee..eeeeeeeee.hhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggi A 254 CHWADTELNRRRRRFCSKVEGYGSVCSCKDPTPIEFSPDPLPDNKVLNVPVAVIAGNRPNYLYRMLRSLLSAQGVSPQMITVFIDGYYEEPMDVVALFGLRGIQHTPISIKNARVSQHYKASLTATFNLFPEAKFAVVLEEDLDIAVDFFSFLSQSIHLLEEDDSLYCISAWNDQGYEHTAEDPALLYRVETMPGLGWVLRRSLYKEELEPKWPTPEKLWDWDMWMRMPEQRRGRECIIPDVSRSYHFGIVGLNMNGYFHEAYFKKHKFNTVPGVQLRNVDSLKKEAYEVEVHRLLSEAEVLDHSKNPCEDSFLPDTEGHTYVAFIRMEKDDDFTTWTQLAKCLHIWDLDVRGNHRGLWRLFRKKNHFLVVGVPASPYSVKKPPSVTPIFLEPP 647
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643    


Chain B from PDB  Type:PROTEIN  Length:551
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeee..eeeeee.......eeeeeee......eeeeeee.....hhhhhhhhhhhh.....eeeeeee.......hhhhhhhhhhh...hhhhh....eeeeeee....eeeeeee...........eeeeeeee.............hhhhhhhhhhhh....hhhhh........................eeeee..hhhhhhhhhhhhh.....hhh.eeeeee..hhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhhhhh....eeeeee..eee..hhhhhhhhhhhhhhhh..eeeee................eeee.......eeeehhhhhhhhhhhh.......hhhhhhhhhhhhh..eeeee....eee........hhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhee........hhhhh......eeeeeeee.....hhhhhhhhhhh.........ee..eeeeee..eeeeeeeee.hhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ggi B  97 RVLDVEVYSSRSKVYVAVDGTTVLEDEAREQGRGIHVIVLNQATGHVMAKRVFDTYSPHEDEAMVLFLNMVAPGRVLICTVKDEGSFHLKDTAKALLRSLGSQAGPALGWRDTWAFVGRKGGPVFGEKHSKSPALSSWGDPVLLKTDVPLSSAEEAECHWADTELNRRRRRFCSKVEGYGSVCSCKDPTPIEFSPDPLPDNKVLNVPVAVIAGNRPNYLYRMLRSLLSAQGVSPQMITVFIDGYYEEPMDVVALFGLRGIQHTPISIKNARVSQHYKASLTATFNLFPEAKFAVVLEEDLDIAVDFFSFLSQSIHLLEEDDSLYCISAWNDQGYEHTAEDPALLYRVETMPGLGWVLRRSLYKEELEPKWPTPEKLWDWDMWMRMPEQRRGRECIIPDVSRSYHFGIVGLNMNGYFHEAYFKKHKFNTVPGVQLRNVDSLKKEAYEVEVHRLLSEAEVLDHSKNPCEDSFLPDTEGHTYVAFIRMEKDDDFTTWTQLAKCLHIWDLDVRGNHRGLWRLFRKKNHFLVVGVPASPYSVKKPPSVTPIFLEPP 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       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646 


Chain F from PDB  Type:PROTEIN  Length:10
                                          
               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
                 5ggi F   0 xAAPTPVAAP   9
                            |        9
                            0-ACE     


Chain G 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
                 5ggi G   1 AAPTP   5
   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 5GGI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

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