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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL) ASPARAGINE AMIDASE AT 2.2 ANGSTROMS RESOLUTION
 
Authors :  P. Van Roey, P. Kuhn
Date :  02 Jun 94  (Deposition) - 30 Nov 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kuhn, A. L. Tarentino, T. H. Plummer Jr. , P. Van Roey
Crystal Structure Of Peptide-N4-(N-Acetyl-Beta-D-Glucosaminyl) Asparagine Amidase F At 2. 2-A Resolution.
Biochemistry V. 33 11699 1994
PubMed-ID: 7918386  |  Reference-DOI: 10.1021/BI00205A005
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL) ASPARAGINE AMIDASE F
    Chains: A
    EC Number: 3.5.1.52
    Engineered: YES
    Organism Scientific: ELIZABETHKINGIA MENINGOSEPTICA
    Organism Taxid: 238

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PNG)

(-) Sites  (0, 0)

(no "Site" information available for 1PNG)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:51 -A:56
2A:204 -A:208
3A:231 -A:252

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Lys A:195 -Pro A:196
2Cys A:204 -Ala A:205
3Ser A:240 -Pro A:241

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PNG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PNG)

(-) Exons   (0, 0)

(no "Exon" information available for 1PNG)

(-) 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:310
 aligned with PNGF_ELIMR | P21163 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:310
                                    54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354
           PNGF_ELIMR    45 NTVNIKTFDKVKNAFGDGLSQSAEGTFTFPADVTTVKTIKMFIKNECPNKTCDEWDRYANVYVKNKTTGEWYEIGRFITPYWVGTEKLPRGLEIDVTDFKSLLSGNTELKIYTETWLAKGREYSVDFDIVYGTPDYKYSAVVPVIQYNKSSIDGVPYGKAHTLGLKKNIQLPTNTEKAYLRTTISGWGHAKPYDAGSRGCAEWCFRTHTIAINNANTFQHQLGALGCSANPINNQSPGNWAPDRAGWCPGMAVPTRIDVLNNSLTGSTFSYEYKFQSWTNNGTNGDAFYAISSFVIAKSNTPISAPVVTN 354
               SCOP domains d1pnga1 A:5-140 Peptide:N-glycosidase F, PNGase F                                                                                       d1pnga2 A:141-314 Peptide:N-glycosidase F, PNGase F                                                                                                                            SCOP domains
               CATH domains 1pngA01 A:5-139  [code=2.60.120.230, no name defined]                                                                                  1pngA02 A:140-314  [code=2.60.120.230, no name defined]                                                                                                                         CATH domains
               Pfam domains ---N-glycanase_N-1pngA02 A:8-133                                                                                                 -------N-glycanase_C-1pngA01 A:141-300                                                                                                                                 -------------- Pfam domains
     Sec.struct. author (1) eeeeeeeeeeeeeee.....eeeeeeeee.......eeeeeeee..hhhhh.....eeeeeeee.....eeeeeeeeee............eeeeehhhh.....eeeeeeeee......eeeeeeeeeeee.....------------hhhhh---........eeeee.......eeeeeeeeee..................eeeeeee.....eeeee...hhhhh.........................-----hhhhh..eeeeeee............eeeeeeeeeeeee........... Sec.struct. author (1)
     Sec.struct. author (2) -----------------------------------------------------------------------------------------------------------------------------------------eeeeeeeeeeeeeeeeeeee--------------------------------------------------------------------------------------------------eeeeeeeeee--------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1png A   5 NTVNIKTFDKVKNAFGDGLSQSAEGTFTFPADVTTVKTIKMFIKNECPNKTCDEWDRYANVYVKNKTTGEWYEIGRFITPYWVGTEKLPRGLEIDVTDFKSLLSGNTELKIYTETWLAKGREYSVDFDIVYGTPDYKYSAVVPVIQYNKSSIDGVPYGKAHTLGLKKNIQLPTNTEKAYLRTTISGWGHAKPYDAGSRGCAEWCFRTHTIAINNANTFQHQLGALGCSANPINNQSPGNWAPDRAGWCPGMAVPTRIDVLNNSLTGSTFSYEYKFQSWTNNGTNGDAFYAISSFVIAKSNTPISAPVVTN 314
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: N-glycanase_C] (4)
(-)
Clan: no clan defined [family: N-glycanase_N] (4)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PNGF_ELIMR | P21163)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016715    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced ascorbate and one other donor, and one atom of oxygen is incorporated into one donor.
    GO:0000224    peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase activity    Catalysis of the reaction: 4-N-(N-acetyl-D-glucosaminyl)-protein + H2O = N-acetyl-beta-D-glucosaminylamine + peptide L-aspartate. This reaction is the hydrolysis of an N4-(acetyl-beta-D-glucosaminyl)asparagine residue in which the N-acetyl-D-glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D-glucosaminylamine and the peptide containing an aspartic residue.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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    Cys A:204 - Ala A:205   [ RasMol ]  
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        PNGF_ELIMR | P21163: 1pgs 1pnf

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