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(-) Description

Title :  THE ACTIVE SITE OF O-GLCNAC TRANSFERASE IMPOSES CONSTRAINTS ON SUBSTRATE SEQUENCE
 
Authors :  S. Pathak, J. Alonso, M. Schimpl, K. Rafie, D. E. Blair, V. S. Borodkin, O. Albarbarawi, D. M. F. Van Aalten
Date :  26 May 15  (Deposition) - 05 Aug 15  (Release) - 16 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,D
Keywords :  O-Glcnac Transferase, Glycosyl Transferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Pathak, J. Alonso, M. Schimpl, K. Rafie, D. E. Blair, V. S. Borodkin, A. W. Schuttelkopf, O. Albarbarawi, D. M. Van Aalten
The Active Site Of O-Glcnac Transferase Imposes Constraints On Substrate Sequence.
Nat. Struct. Mol. Biol. V. 22 744 2015
PubMed-ID: 26237509  |  Reference-DOI: 10.1038/NSMB.3063

(-) Compounds

Molecule 1 - UDP-N-ACETYLGLUCOSAMINE--PEPTIDE N- ACETYLGLUCOSAMINYLTRANSFERASE 110 KDA SUBUNIT
    Chains: A
    EC Number: 2.4.1.255
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Fragment: UNP RESIDUES 197-915
    Gene: OGT
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: O-GLCNAC TRANSFERASE SUBUNIT P110,O-LINKED N- ACETYLGLUCOSAMINE TRANSFERASE 110 KDA SUBUNIT,OGT
 
Molecule 2 - LAMINB1 RESIDUES 179-191
    Chains: D
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
112V1Ligand/Ion(2S,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-THIOPYRAN-2-YL [(2R,3S,4R,5R)-5-(2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGENDIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:498 , PRO A:559 , THR A:560 , LEU A:563 , LEU A:653 , PRO A:656 , PHE A:694 , GLN A:839 , TYR A:841 , LYS A:842 , LEU A:866 , VAL A:895 , ALA A:896 , LYS A:898 , HIS A:901 , ARG A:904 , CYS A:917 , HIS A:920 , THR A:921 , THR A:922 , ASP A:925 , HOH A:1205 , HOH A:1222 , HOH A:1227 , HOH A:1240 , HOH A:1271 , SER D:186 , ARG D:187 , VAL D:188 , THR D:189 , HOH D:201binding site for residue 12V A 1101

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:868 -Pro A:869

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BNW)

(-) 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:694
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...........hhhhh..eeeeeee.....hhhhhhhhhhhhhh....eeeeeee......hhhhhhhhhhh.eeee.hhh.hhhhhhhhhhhh...eeee........hhhhhhh....eeee..............eeee.....hhhhhhhh..eeee........hhhhhhhhhh..eee......eeee..hhhhhhhh....eee....eeee..hhhhhhhhhhhhhh..eeee..eeeee..hhhhhhhhhhh.......eeeee.hhhh.....eeeee..hhhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhhhhhhh.hhh.eeeee..hhhhhhhhhh...eee.......hhhhhhhhhh...ee.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5bnw A  314 PTHADSLNNLANIKREQGNIEEAVRLYRKALEVFPEFAAAHSNLASVLQQQGKLQEALMHYKEAIRISPTFADAYSNMGNTLKEMQDVQGALQCYTRAIQINPAFADAHSNLASIHKDSGNIPEAIASYRTALKLKPDFPDAYCNLAHCLQIVCDWTDYDERMKKLVSIVADQLEKNRLPSVHPHHSMLYPLSHGFRKAIAERHGNLCLDKINVLHKPPYEHPKDLKLSDGRLRVGYVSSDFGNHPTSHLMQSIPGMHNPDKFEVFCYALSPDDGTNFRVKVMAEANHFIDLSQIPCNGKAADRIHQDGIHILVNMNGYTKGARNELFALRPAPIQAMWLGYPGTSGALFMDYIITDQETSPAEVAEQYSEKLAYMPHTFFIGDHANMFPHLKKKAVIDIYDNRIVLNGIDLKAFLDSLPDVKIVKMKNMPVIPMNTIAEAVIEMINRGQIQITINGFSISNGLATTQINNKAATGEEVPRTIIVTTRSQYGLPEDAIVYCNFNQLYKIDPSTLQMWANILKRVPNSVLWLLRFPAVGEPNIQQYAQNMGLPQNRIIFSPVAPKEEHVRRGQLADVCLDTPLCNGHTTGMDVLWAGTPMVTMPGETLASRVAASQLTCLGCLELIAKNRQEYEDIAVKLGTDLEYLKKVRGKVWKQRISSPLFNTKQYTMELERLYLQMWEHYAAGNKPDHMIK 1028
                                   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       653       663       673       683       693       703       719       729       739       764       774       784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024    
                                                                                                                                                                                                                                                                                                                                                                                                                                        712|                         747|                                                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                                         719                          763                                                                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:7
                                        
               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
                5bnw D  185 SSRVTVS  191
   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 5BNW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (81, 83)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LMNB2_HUMAN | Q03252: 2lll
        OGT1_HUMAN | O15294: 1w3b 3pe3 3pe4 3tax 4ay5 4ay6 4cdr 4gyw 4gyy 4gz3 4gz5 4gz6 4n39 4n3a 4n3b 4n3c 4xi9 4xif 5c1d 5hgv 5lvv 5lwv

(-) Related Entries Specified in the PDB File

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