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(-) Description

Title :  CPOGA D298N IN COMPLEX WITH DROSOPHILA HCF -DERIVED THR-O-GLCNAC PEPTIDE
 
Authors :  N. Selvan, D. M. F. Van Aalten
Date :  20 May 15  (Deposition) - 23 Sep 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,H
Keywords :  Hydrolase-O-Glcnacylated Peptide Complex Tim Barrel Thr-O-Glcnac, Hydrolase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Mariappa, N. Selvan, V. S. Borodkin, J. Alonso, A. T. Ferenbach, C. Shepherd, I. H. Navratilova, D. M. Van Aalten
A Mutant O-Glcnacase As A Probe To Reveal Global Dynamics O Protein O-Glcnacylation During Drosophila Embryonic Development.
Biochem. J. V. 470 255 2015
PubMed-ID: 26348912  |  Reference-DOI: 10.1042/BJ20150610

(-) Compounds

Molecule 1 - NAG-PRO-SER-THR-ALA-THR-O-GLCNAC CONTAINING PEPTIDE FROM DROSOPHILA HCF
    Chains: H
    Engineered: YES
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Other Details: THR-O-GLCNAC CONTAINING PEPTIDE FROM DROSOPHILA HCF
    Synthetic: YES
 
Molecule 2 - O-GLCNACASE NAGJ
    Chains: A
    EC Number: 3.2.1.169, 3.2.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 39-617
    Gene: NAGJ, CPF_1442
    Organism Scientific: CLOSTRIDIUM PERFRINGENS (STRAIN ATCC 13124 / NCTC 8237 / TYPE A)
    Organism Taxid: 195103
    Synonym: CPOGA,BETA-N-ACETYLGLUCOSAMINIDASE,BETA-N- ACETYLHEXOSAMINIDASE,BETA-HEXOSAMINIDASE,GH84C,HEXOSAMINIDASE B,N- ACETYL-BETA-D-GLUCOSAMINIDASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric/Biological Unit (2, 16)
No.NameCountTypeFull Name
1CD15Ligand/IonCADMIUM ION
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:58 , GLU A:272 , HOH A:857binding site for residue CD A 701
02AC2SOFTWAREGLU A:51 , ASN A:450 , ASP A:452 , HOH A:838binding site for residue CD A 702
03AC3SOFTWAREASP A:139 , GLU A:170binding site for residue CD A 703
04AC4SOFTWARELEU A:68 , GLU A:71 , HOH A:843 , HOH A:849binding site for residue CD A 704
05AC5SOFTWAREGLU A:73 , GLU A:108 , ASP A:111 , HOH A:803 , HOH A:861binding site for residue CD A 705
06AC6SOFTWAREASP A:117 , GLU A:145 , GLU A:545 , HOH A:840 , HOH A:867binding site for residue CD A 706
07AC7SOFTWAREASP A:139 , ASP A:268binding site for residue CD A 707
08AC8SOFTWAREASP A:150 , ASP A:252binding site for residue CD A 708
09AC9SOFTWAREGLU A:272 , HIS A:276binding site for residue CD A 709
10AD1SOFTWAREGLU A:282 , ASP A:286 , GLU A:588 , HOH A:807binding site for residue CD A 710
11AD2SOFTWAREGLU A:362 , ASP A:424binding site for residue CD A 711
12AD3SOFTWAREHIS A:413 , HOH A:856binding site for residue CD A 712
13AD4SOFTWAREASP A:112 , GLU A:550binding site for residue CD A 713
14AD5SOFTWAREASP A:117 , GLU A:545 , GLU A:549binding site for residue CD A 714
15AD6SOFTWAREASP A:474 , ARG A:531 , GLU A:534binding site for residue CD A 715
16AD7SOFTWAREGLY A:187 , PHE A:188 , TYR A:189 , LYS A:218 , ASP A:297 , ASN A:298 , TYR A:335 , VAL A:370 , TRP A:394 , ASN A:396 , ASP A:401 , ASN A:429 , SER H:616 , THR H:617binding site for Mono-Saccharide NAG H 701 bound to THR H 617

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZXL)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Asn A:47 -Pro A:48
2Tyr A:397 -Pro A:398

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZXL)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZXL)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZXL)

(-) 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:579
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeee....ee...eeeee.....hhhhhhhhhhhhhhh..ee........eeeeeee....hhhhhhhh............eeeeee..eeeeee.hhhhhhhhhhhhhhhh...ee..eeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhhhh....eeeee.......hhhhhhhhhhhhhhhhhhhhh.....eee....hhhhhee..eehhhhhhhhhhh....eeee..........hhhhhhhhhhhhh..eeeee......................hhhh.eeeeee....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhh....ee.....ee....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zxl A  39 NQVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANNIEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGDGTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKLNTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAGEEDFNHLITKAESLYDMGVRSFAIYWDNIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLITVPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYDRNMAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWNMDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWNKLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLDMIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEAL 617
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608         


Chain H from PDB  Type:PROTEIN  Length:4
                                    
               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
                 4zxl H 615 PSTA 618
   Legend:   → Mismatch (orange background)
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  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 4ZXL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZXL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZXL)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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    Asn A:47 - Pro A:48   [ RasMol ]  
    Tyr A:397 - Pro A:398   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        OGA_CLOP1 | Q0TR53: 2cbi 2cbj 2j1a 2j1e 2j62 2j7m 2jh2 2o4e 2ozn 2v5c 2v5d 2vur 2w1n 2wb5 2x0y 2xpk 2ydq 2ydr 2yds

(-) Related Entries Specified in the PDB File

2vur 2VUR CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT LIGAND
2ydq 2YDQ CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT LIGAND
2ydr 2YDR CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT LIGAND
2yds 2YDS CONTAINS THE SAME PROTEIN COMPLEXED WITH A DIFFERENT LIGAND