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(-) Description

Title :  PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE
 
Authors :  P. Van Roey, P. Kuhn
Date :  11 Oct 95  (Deposition) - 08 Mar 96  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Kuhn, C. Guan, T. Cui, A. L. Tarentino, T. H. Plummer Jr. , P. Van Roe
Active Site And Oligosaccharide Recognition Residues Of Peptide-N4-(N-Acetyl-Beta-D-Glucosaminyl)Asparagine Amidase F.
J. Biol. Chem. V. 270 29493 1995
PubMed-ID: 7493989  |  Reference-DOI: 10.1074/JBC.270.49.29493
(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
    Organism Scientific: ELIZABETHKINGIA MENINGOSEPTICA
    Organism Taxid: 238
    Synonym: PNGASE F

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:59 , ASP A:60 , ARG A:61 , TRP A:191 , NAG A:432 , HOH A:544 , HOH A:573 , HOH A:654BINDING SITE FOR RESIDUE NDG A 431
2AC2SOFTWAREARG A:61 , GLU A:118 , TRP A:120 , ALA A:164 , NDG A:431 , HOH A:697 , HOH A:698 , HOH A:745BINDING SITE FOR RESIDUE NAG A 432
3AC3SOFTWARELYS A:41 , PRO A:138 , ASP A:139 , TYR A:140 , LYS A:302 , HOH A:622 , HOH A:626BINDING SITE FOR RESIDUE SO4 A 500

(-) 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 1PNF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PNF)

(-) 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:314
 aligned with PNGF_ELIMR | P21163 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:314
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350    
           PNGF_ELIMR    41 APADNTVNIKTFDKVKNAFGDGLSQSAEGTFTFPADVTTVKTIKMFIKNECPNKTCDEWDRYANVYVKNKTTGEWYEIGRFITPYWVGTEKLPRGLEIDVTDFKSLLSGNTELKIYTETWLAKGREYSVDFDIVYGTPDYKYSAVVPVIQYNKSSIDGVPYGKAHTLGLKKNIQLPTNTEKAYLRTTISGWGHAKPYDAGSRGCAEWCFRTHTIAINNANTFQHQLGALGCSANPINNQSPGNWAPDRAGWCPGMAVPTRIDVLNNSLTGSTFSYEYKFQSWTNNGTNGDAFYAISSFVIAKSNTPISAPVVTN 354
               SCOP domains d1pnfa1 A:1-140 Peptide:N-glycosidase F, PNGase F                                                                                           d1pnfa2 A:141-314 Peptide:N-glycosidase F, PNGase F                                                                                                                            SCOP domains
               CATH domains ----1pnfA01 A:5-139  [code=2.60.120.230, no name defined]                                                                                  1pnfA02 A:140-314  [code=2.60.120.230, no name defined]                                                                                                                         CATH domains
               Pfam domains -------N-glycanase_N-1pnfA02 A:8-133                                                                                                 -------N-glycanase_C-1pnfA01 A:141-300                                                                                                                                 -------------- Pfam domains
     Sec.struct. author (1) eeeeeeeeeeeeeeeeeee.....eeeeeeeee.......eeeeeeee...hhh......eeeeeeee.....eeeeeeeeee............eeeeehhh......eeeeeeeee......eeeeeeeeeeee.....-------------hhh----........eeeee.......eeeeeeeeee..................eeeeeee.....eeeee....hhh..........................------hhh-..eeeeeee............eeeeeeeeeeeee........... Sec.struct. author (1)
     Sec.struct. author (2) ---------------------------------------------------------------------------------------------------------------------------------------------eeeeeeeeeeeeeeeeeeee--------------------------------------------------------------------------------------------------eeeeeeeeee--------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pnf A   1 APADNTVNIKTFDKVKNAFGDGLSQSAEGTFTFPADVTTVKTIKMFIKNECPNKTCDEWDRYANVYVKNKTTGEWYEIGRFITPYWVGTEKLPRGLEIDVTDFKSLLSGNTELKIYTETWLAKGREYSVDFDIVYGTPDYKYSAVVPVIQYNKSSIDGVPYGKAHTLGLKKNIQLPTNTEKAYLRTTISGWGHAKPYDAGSRGCAEWCFRTHTIAINNANTFQHQLGALGCSANPINNQSPGNWAPDRAGWCPGMAVPTRIDVLNNSLTGSTFSYEYKFQSWTNNGTNGDAFYAISSFVIAKSNTPISAPVVTN 314
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   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  (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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 Related Entries

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

UniProtKB/Swiss-Prot
        PNGF_ELIMR | P21163: 1pgs 1png

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PNF)