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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CORE CATALYTIC DOMAIN OF HUMAN O-GLCNACASE
 
Authors :  D. J. Klein, N. L. Elsen
Date :  11 Jan 17  (Deposition) - 29 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.97
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, O-Glcnacase, Gh84, Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. L. Elsen, S. B. Patel, R. E. Ford, D. L. Hall, F. Hess, H. Kandula, M. Kornienko, K. J. Lumb, J. Reid, H. Selnick, J. M. Shipman, S. Sharma, S. M. Soisson, D. J. Klein
Crystal Structure Of The Core Catalytic Domain Of Human O-Glcnacase And Molecular Basis Of Activity And Inhibition
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - O-GLCNACASE TIM-BARREL DOMAIN
    Chains: A, C
    EC Number: 3.2.1.169, 3.2.1.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: MGEA5, HEXC, KIAA0679, MEA5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: OGA,BETA-N-ACETYLGLUCOSAMINIDASE,BETA-N- ACETYLHEXOSAMINIDASE,BETA-HEXOSAMINIDASE,MENINGIOMA-EXPRESSED ANTIGEN 5,N-ACETYL-BETA-D-GLUCOSAMINIDASE,N-ACETYL-BETA-GLUCOSAMINIDASE, NUCLEAR CYTOPLASMIC O-GLCNACASE AND ACETYLTRANSFERASE,NCOAT
 
Molecule 2 - O-GLCNACASE STALK DOMAIN
    Chains: B, D
    EC Number: 3.2.1.169, 3.2.1.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: MGEA5, HEXC, KIAA0679, MEA5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: OGA,BETA-N-ACETYLGLUCOSAMINIDASE,BETA-N- ACETYLHEXOSAMINIDASE,BETA-HEXOSAMINIDASE,MENINGIOMA-EXPRESSED ANTIGEN 5,N-ACETYL-BETA-D-GLUCOSAMINIDASE,N-ACETYL-BETA-GLUCOSAMINIDASE, NUCLEAR CYTOPLASMIC O-GLCNACASE AND ACETYLTRANSFERASE,NCOAT

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:174 , TYR A:219 , THR A:250 , TRP A:278 , ASN A:280 , GOL A:502binding site for residue GOL A 501
2AC2SOFTWAREGLY A:67 , PHE A:68 , LYS A:98 , ASP A:285 , ASN A:313 , GOL A:501binding site for residue GOL A 502
3AC3SOFTWAREGLY C:67 , ASP C:174 , TYR C:219 , TRP C:278 , ASN C:280binding site for residue GOL C 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:225 -Pro A:226
2Tyr C:225 -Pro C:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UHK)

(-) 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:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhhhhhhhhhhh...eeee................hhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhhh....eeeee........hhhhhhhh.hhhhhhhhhhhhhhhhh.....eeee....hhhhh......hhhhhhhhhhh...eeeee..........hhhhhhhhhhhhh...eeee....hhhhh...........hhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uhk A  58 RRFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRVLYSPQMALKLALTEWLQEFG 392
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337  ||   378       388    
                                                                                                                                                                                                                                                                                                                    340|                    
                                                                                                                                                                                                                                                                                                                     372                    


Chain B from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 5uhk B 543 MEKPLYTAEPVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRRGGLAGEFQRLLP 694
                                   552       562       572       582       607       617       627       637       647       657      |684       694
                                                                         590|                                                       664|            
                                                                          606                                                        682            


Chain C from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhhhhhhhhhhh...eeee................hhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh...eeeee........hhhhhhhh.hhhhhhhhhhhhhhhhh.....eeee...............hhhhhhhhhhh....eeee..........hhhhhhhhhhhhh...eeee....hhhhh...........hhhhhhhh.eeee....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uhk C  58 RRFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDIDHNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVLYSPQMALKLALTEWLQEFG 392
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337||     380       390  
                                                                                                                                                                                                                                                                                                                  338|                    
                                                                                                                                                                                                                                                                                                                   372                    


Chain D from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 5uhk D 543 MEKPLYTAEPVTLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWLGCRGGLAGEFQRLLP 694
                                   552       562       572       582      |606       616       626       636       646       656      |684       694
                                                                        589|                                                        663|            
                                                                         604                                                         682
   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 5UHK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  5uhk
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  3.2.1.169
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 Related Entries

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

UniProtKB/Swiss-Prot
        OGA_HUMAN | O60502: 2ydq 5m7r 5m7s 5m7t 5m7u 5tke 5uhl 5uho 5uhp 5un8 5un9

(-) Related Entries Specified in the PDB File

5uhl 5uho 5uhp