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(-) Description

Title :  THE THREE-DIMENSIONAL STRUCTURE OF PNGASE F, A GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
 
Authors :  G. E. Norris, T. J. Stillman, B. F. Anderson, E. N. Baker
Date :  06 Oct 94  (Deposition) - 26 Jan 95  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Endoglycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. E. Norris, T. J. Stillman, B. F. Anderson, E. N. Baker
The Three-Dimensional Structure Of Pngase F, A Glycosylasparaginase From Flavobacterium Meningosepticum.
Structure V. 2 1049 1994
PubMed-ID: 7881905  |  Reference-DOI: 10.1016/S0969-2126(94)00108-1
(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 1PGS)

(-) Sites  (0, 0)

(no "Site" information available for 1PGS)

(-) 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 1PGS)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1PGS)

(-) 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:311
 aligned with PNGF_ELIMR | P21163 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:311
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353 
           PNGF_ELIMR    44 DNTVNIKTFDKVKNAFGDGLSQSAEGTFTFPADVTTVKTIKMFIKNECPNKTCDEWDRYANVYVKNKTTGEWYEIGRFITPYWVGTEKLPRGLEIDVTDFKSLLSGNTELKIYTETWLAKGREYSVDFDIVYGTPDYKYSAVVPVIQYNKSSIDGVPYGKAHTLGLKKNIQLPTNTEKAYLRTTISGWGHAKPYDAGSRGCAEWCFRTHTIAINNANTFQHQLGALGCSANPINNQSPGNWAPDRAGWCPGMAVPTRIDVLNNSLTGSTFSYEYKFQSWTNNGTNGDAFYAISSFVIAKSNTPISAPVVTN 354
               SCOP domains d1pgsa1 A:4-140 Peptide:N-glycosidase F, PNGase F                                                                                        d1pgsa2 A:141-314 Peptide:N-glycosidase F, PNGase F                                                                                                                            SCOP domains
               CATH domains -1pgsA01 A:5-139  [code=2.60.120.230, no name defined]                                                                                  1pgsA02 A:140-314  [code=2.60.120.230, no name defined]                                                                                                                         CATH domains
               Pfam domains ----N-glycanase_N-1pgsA02 A:8-133                                                                                                 -------N-glycanase_C-1pgsA01 A:141-300                                                                                                                                 -------------- Pfam domains
         Sec.struct. author ..eeeee....eee........eeeeeeee......eeeeeeeeee.hhhhh......eeeeeee......eeeeeeee.............eeee.hhhh....eeeeeeeee.......eeeeeeeeeee......eeeeeeeeee..hhhhhee.........eeeee......eeeeeeeeeee.eeeeee...eeee....eeeeeee..eeeeeeee...hhhhh.........................eeee.hhhhh..eeeeeee.............eeeeeeeeeeee.......eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pgs A   4 DNTVNIKTFDKVKNAFGDGLSQSAEGTFTFPADVTTVKTIKMFIKNECPNKTCDEWDRYANVYVKNKTTGEWYEIGRFITPYWVGTEKLPRGLEIDVTDFKSLLSGNTELKIYTETWLAKGREYSVDFDIVYGTPDYKYSAVVPVIQYNKSSIDGVPYGKAHTLGLKKNIQLPTNTEKAYLRTTISGWGHAKPYDAGSRGCAEWCFRTHTIAINNANTFQHQLGALGCSANPINNQSPGNWTPDRAGWCPGMAVPTRIDVLNNSLTGSTFSYEYKFQSWTNNGTNGDAFYAISSFVIAKSNTPISAPVVTN 314
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313
   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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  Cis Peptide Bonds
    Cys A:204 - Ala A:205   [ RasMol ]  
    Lys A:195 - Pro A:196   [ RasMol ]  
    Ser A:240 - Pro A:241   [ RasMol ]  
 

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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