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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 :  2.79
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,F,G  (1x)
Biol. Unit 2:  C,D,E,H  (1x)
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, B, C, 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
 
Molecule 2 - O-GLCNACASE STALK DOMAIN
    Chains: E, F, G, H
    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

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB   FG 
Biological Unit 2 (1x):   CDE  H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:98 , ASP A:174 , TYR A:219 , THR A:250 , VAL A:254 , TRP A:278 , ASN A:280binding site for residue GOL A 501
2AC2SOFTWARELYS B:98 , ASP B:174 , ASP B:175 , TYR B:219 , THR B:250 , TRP B:278 , ASN B:280binding site for residue GOL B 501
3AC3SOFTWARELYS C:98 , ASP C:174 , CYS C:215 , TYR C:219 , THR C:250 , TRP C:278 , ASN C:280binding site for residue GOL C 501
4AC4SOFTWARELYS D:98 , ASP D:174 , CYS D:215 , TYR D:219 , THR D:250 , TRP D:278 , ASN D:280binding site for residue GOL D 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:225 -Pro A:226
2Tyr B:225 -Pro B:226
3Tyr C:225 -Pro C:226
4Tyr D:225 -Pro D:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UHP)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               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....eeee..........hhhhhhhhhh......eeee....................hhhhhhhh.eeee....hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uhp A  59 RFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDINMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRDVLYSPQMALKLALTEWLQEFGVPHQY 397
                                    68        78        88        98       108       118       128       138       148       158       168       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340|      380       390       
                                                                                                                                               176|                                                                                                                                                              340|                          
                                                                                                                                                179                                                                                                                                                               371                          


Chain B from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               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....................hhhhhhhh.eeee....hhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uhp B  59 RFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDDINMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRDVLYSPQMALKLALTEWLQEFGVPHQY 397
                                    68        78        88        98       108       118       128       138       148       158       168       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340|      380       390       
                                                                                                                                               176|                                                                                                                                                              340|                          
                                                                                                                                                179                                                                                                                                                               371                          


Chain C from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.......hhhhhhhhhhhhhhh...eeee................hhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhh...eeeee...hhhhhh...hhhhhhhhhhhhhhhhh.....eeee...............hhhhhhhhhhh....eeee..........hhhhhhhhhhhhh...eeee....................hhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uhp C  49 AVAGAAGGARRFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRTDVLYSPQMALKLALTEWLQEFG 392
                                    58        68        78        88        98       108       118       128       138       148       158       168     ||183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333      |372       382       392
                                                                                                                                                       174|                                                                                                                                                             340|                      
                                                                                                                                                        180                                                                                                                                                              370                      


Chain D from PDB  Type:PROTEIN  Length:310
                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeee.......hhhhhhhhhhhhhhh...eeee................hhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhhh....eeeee....hhhhhh...hhhhhhhhhhhhhhhhh.....eeee....hhhhh......hhhhhhhhhhh....eeee..........hhhhhhhhhhhhh...eeee....................hhhhhhhh.eeee....hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uhp D  50 VAGAAGGARRFLCGVVEGFYGRPWVMEQRKELFRRLQKWELNTYLYAPKDDYKHRMFWREMYSVEEAEQLMTLISAAREYEIEFIYAISPGLDITFSNPKEVSTLKRKLDQVSQFGCRSFALLFDNMCAADKEVFSSFAHAQVSITNEIYQYLGEPETFLFCPTEYCGTFCYPNVSQSPYLRTVGEKLLPGIEVLWTGPKVVSKEIPVESIEEVSKIIKRAPVIWDNIHANDYDQKRLFLGPYKGRSTELIPRLKGVLTNPNCEFEANYVAIHTLATWYKSNMNGVRTDVLYSPQMALKLALTEWLQEFG 392
                                    59        69        79        89        99       109       119       129       139       149       159       169    || 183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333      |372       382       392
                                                                                                                                                      174|                                                                                                                                                              340|                      
                                                                                                                                                       179                                                                                                                                                               370                      


Chain E from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5uhp E 554 TLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQEPWAFRGGLAGEFQRLL 693
                                   563       573       583     ||604       614       624       634       644       654    || 681       691  
                                                             589|                                                       659|                
                                                              601                                                        677                


Chain F from PDB  Type:PROTEIN  Length:109
                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 5uhp F 554 TLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWRGGLAGEFQRLLPI 695
                                   563       573       583     ||605       615       625       635       645       655    || 686         
                                                             589|                                                       660|             
                                                              602                                                        682             


Chain G from PDB  Type:PROTEIN  Length:114
                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 5uhp G 554 TLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRANKDSEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWWAFRGGLAGEFQRLLPI 695
                                   563       573       583    || 603       613       623       633       643       653      |681       691    
                                                            588|                                                          660|                
                                                             599                                                           679                


Chain H from PDB  Type:PROTEIN  Length:112
                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh......hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                 5uhp H 554 TLEDLQLLADLFYLPYEHGPKGAQMLREFQWLRASEKIEEWRSRAAKFEEMCGLVMGMFTRLSNCANRTILYDMYSYVWDIKSIMSMVKSFVQWQEPWAFRGGLAGEFQRLL 693
                                   563       573       583   ||  606       616       626       636       646       656   ||  681       691  
                                                           587|                                                        660|                 
                                                            601                                                         676
   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 5UHP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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  5uhp
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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 5uhk 5uhl 5uho 5un8 5un9

(-) Related Entries Specified in the PDB File

5uhk 5uhl 5uho