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(-) Description

Title :  RECOMBINANT PEPTIDE: N-GLYCANASE F (PNGASE F)
 
Authors :  J. Filitcheva, B. F. Anderson, G. E. Norris
Date :  17 Nov 10  (Deposition) - 26 Jan 11  (Release) - 26 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.57
Chains :  Asym./Biol. Unit :  A
Keywords :  Jelly Roll Fold, N-Glycanase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Filitcheva, B. F. Anderson, G. E. Norris
Recombinant Peptide:N-Glycanase F (Pngase F)
To Be Published
PubMed: search

(-) Compounds

Molecule 1
    Chains: A
    EC Number: 3.5.1.52
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: OPH6
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PNG
    Organism Common: CHRYSEOBACTERIUM MENINGOSEPTICUM
    Organism Scientific: ELIZABETHKINGIA MENINGOSEPTICA
    Organism Taxid: 238
    Strain: CDC 3552

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric/Biological Unit (3, 14)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL10Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:41 , PRO A:138 , ASP A:139 , TYR A:140 , LYS A:302 , HOH A:463 , HOH A:487 , HOH A:556 , HOH A:622 , HOH A:639BINDING SITE FOR RESIDUE SO4 A 324
02AC2SOFTWAREGLY A:200 , THR A:272 , HOH A:358 , HOH A:726BINDING SITE FOR RESIDUE SO4 A 325
03AC3SOFTWAREASP A:60 , TYR A:85 , ASN A:243 , GOL A:335 , HOH A:417 , HOH A:491BINDING SITE FOR RESIDUE GOL A 326
04AC4SOFTWARETHR A:32 , ASN A:110 , HOH A:380BINDING SITE FOR RESIDUE GOL A 327
05AC5SOFTWARETYR A:161 , GLY A:162 , GLN A:280 , ASN A:281 , TRP A:282 , HOH A:418 , HOH A:617 , HOH A:695BINDING SITE FOR RESIDUE GOL A 328
06AC6SOFTWAREGLN A:174 , LEU A:175 , PRO A:176 , THR A:177 , ARG A:202 , PRO A:246 , SER A:308 , HOH A:408 , HOH A:649 , HOH A:696BINDING SITE FOR RESIDUE GOL A 329
07AC7SOFTWARELEU A:229 , MET A:255 , HOH A:383 , HOH A:502 , HOH A:716BINDING SITE FOR RESIDUE GOL A 330
08AC8SOFTWAREPRO A:138 , LYS A:141 , ILE A:156 , ASN A:304 , HOH A:499 , HOH A:628BINDING SITE FOR RESIDUE GOL A 331
09AC9SOFTWAREARG A:61 , GLU A:118 , SER A:155 , TRP A:191 , GOL A:335 , HOH A:495 , HOH A:628BINDING SITE FOR RESIDUE GOL A 332
10BC1SOFTWARELYS A:181 , TYR A:183 , HOH A:403 , HOH A:452 , HOH A:487 , HOH A:605 , HOH A:619BINDING SITE FOR RESIDUE GOL A 333
11BC2SOFTWARELYS A:10 , LYS A:48 , ARG A:94 , ASP A:130 , HOH A:512 , HOH A:689 , HOH A:732 , HOH A:737BINDING SITE FOR RESIDUE GOL A 334
12BC3SOFTWAREASP A:60 , TRP A:191 , GLU A:206 , GOL A:326 , GOL A:332 , HOH A:467 , HOH A:495BINDING SITE FOR RESIDUE GOL A 335
13BC4SOFTWAREASP A:132 , VAL A:134 , HOH A:691BINDING SITE FOR RESIDUE ACT A 336
14BC5SOFTWAREGLN A:174 , GLY A:200 , SER A:201 , HOH A:707BINDING SITE FOR RESIDUE ACT A 337

(-) 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 3PMS)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PMS)

(-) Exons   (0, 0)

(no "Exon" information available for 3PMS)

(-) 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:312
 aligned with Q9XBM8_ELIME | Q9XBM8 from UniProtKB/TrEMBL  Length:314

    Alignment length:312
                                                                                                                                                                                                                                                                                                                                                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| 
         Q9XBM8_ELIME     4 DNTVNIKTFDKVKNAFGDGLSQSAEGTFTFPADVTAVKTIKMFIKNECPNKTCDEWDRYANVYVKNKTTGEWYEIGRFITPYWVGTEKLPRGLEIDVTDFKSLLSGNTELKIYTETWLAKGREYSVDFDIVYGTPDYKYSAVVPVVQYNKSSIDGVPYGKAHTLALKKNIQLPTNTEKAYLRTTISGWGHAKPYDAGSRGCAEWCFRTHTIAINNSNTFQHQLGALGCSANPINNQSPGNWTPDRAGWCPGMAVPTRIDVLNNSLIGSTFSYEYKFQNWTNNGTNGDAFYAISSFVIAKSNTPISAPVVTN-   -
               SCOP domains d3pmsa1 A:4-140 automated matches                                                                                                        d3pmsa2 A:141-315 automated matches                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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....................ee...eeee.hhhhh..eeeeeee.............eeeeeeeeeeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3pms A   4 DNTVNIKTFDKVKNAFGDGLSQSAEGTFTFPADVTAVKTIKMFIKNECPNKTCDEWDRYANVYVKNKTTGEWYEIGRFITPYWVGTEKLPRGLEIDVTDFKSLLSGNTELKIYTETWLAKGREYSVDFDIVYGTPDYKYSAVVPVVQYNKSSIDGVPYGKAHTLALKKNIQLPTNTEKAYLRTTISGWGHAKPYDAGSRGCAEWCFRTHTIAINNSNTFQHQLGALGCSANPINNQSPGNWTPDRAGWCPGMAVPTRIDVLNNSLIGSTFSYEYKFQNWTNNGTNGDAFYAISSFVIAKSNTPISAPVVTNL 315
                                    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  (0, 0)

(no "CATH Domain" information available for 3PMS)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PMS)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9XBM8_ELIME | Q9XBM8)
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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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

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(-) Related Entries Specified in the PDB File

1pgs NATIVE PNGASE F
1pnf PNGASE F COMPLEX WITH DI-N-ACETYLCHITOBIOSE
1png NATIVE PNGASE F