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(-) Description

Title :  CRYSTAL STRUCTURE OF GLYCOSYLASPARAGINASE-SUBSTRATE COMPLEX
 
Authors :  Y. Wang, H. C. Guo
Date :  04 Apr 06  (Deposition) - 13 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Glycosylasparaginase, Enzyme-Substrate Complex, Catalytic Mechanism, Proton-Relay Network, Electron-Pair Transfer, Nucleophilic Attack, Oxyanion Hole, Enzyme-Acyl Intermediate, Ntn-Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wang, H. C. Guo
Crystallographic Snapshot Of A Productive Glycosylasparaginase-Substrate Complex.
J. Mol. Biol. V. 366 82 2007
PubMed-ID: 17157318  |  Reference-DOI: 10.1016/J.JMB.2006.09.051

(-) Compounds

Molecule 1 - GLYCOSYLASPARAGINASE ALPHA CHAIN
    Chains: A, C
    EC Number: 3.5.1.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2
    Expression System Strain: TB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 46-196
    Organism Scientific: ELIZABETHKINGIA MENINGOSEPTICA
    Organism Taxid: 238
 
Molecule 2 - GLYCOSYLASPARAGINASE BETA CHAIN
    Chains: B, D
    EC Number: 3.5.1.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2
    Expression System Strain: TB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 197-340
    Mutation: YES
    Organism Scientific: ELIZABETHKINGIA MENINGOSEPTICA
    Organism Taxid: 238

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ASN2Mod. Amino AcidASPARAGINE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:11 , PHE A:13 , SER A:50 , HOH A:955 , CYS B:152 , GLY B:204 , ASN B:297 , HOH B:770BINDING SITE FOR RESIDUE NAG A 296
2AC2SOFTWARETRP C:311 , PHE C:313 , SER C:350 , HOH C:642 , HOH C:717 , HOH C:831 , HOH C:931 , CYS D:452 , GLY D:504 , ASN D:597BINDING SITE FOR RESIDUE NAG C 596
3AC3SOFTWARENAG A:296 , CYS B:152 , GLY B:172 , ARG B:180 , ASP B:183 , THR B:203 , GLY B:204 , GLY B:206 , HOH B:629 , HOH B:770BINDING SITE FOR RESIDUE ASN B 297
4AC4SOFTWARENAG C:596 , HOH C:612 , HOH C:717 , CYS D:452 , GLY D:472 , ARG D:480 , ASP D:483 , SER D:484 , THR D:503 , GLY D:504 , GLY D:506 , HOH D:744BINDING SITE FOR RESIDUE ASN D 597

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GL9)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys A:4 -Pro A:5
2Lys C:304 -Pro C:305

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GL9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GL9)

(-) Exons   (0, 0)

(no "Exon" information available for 2GL9)

(-) 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:140
 aligned with ASPG_ELIMR | Q47898 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:140
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186
           ASPG_ELIMR    47 TNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQY 186
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...................eeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gl9 A   2 TNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQY 141
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141


Chain B from PDB  Type:PROTEIN  Length:145
 aligned with ASPG_ELIMR | Q47898 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:145
                                                                                                                                                                         340 
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336   | 
           ASPG_ELIMR   197 TIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALK-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeeee....eeeeeee....eeeee..eeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gl9 B 152 CIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALKN 297
                                   161       171       181       191       201       211       221       231       241       251       261       271       281       291   ||
                                                                                                                                                                         295|
                                                                                                                                                                          297


Chain C from PDB  Type:PROTEIN  Length:142
 aligned with ASPG_ELIMR | Q47898 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:142
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186  
           ASPG_ELIMR    47 TNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQYKP 188
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...................eeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gl9 C 302 TNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQYKP 443
                                   311       321       331       341       351       361       371       381       391       401       411       421       431       441  


Chain D from PDB  Type:PROTEIN  Length:145
 aligned with ASPG_ELIMR | Q47898 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:145
                                                                                                                                                                         340 
                                   206       216       226       236       246       256       266       276       286       296       306       316       326       336   | 
           ASPG_ELIMR   197 TIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALK-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeeee....eeeee......eeeee..eeeee..ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gl9 D 452 CIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALKN 597
                                   461       471       481       491       501       511       521       531       541       551       561       571       581       591   ||
                                                                                                                                                                         595|
                                                                                                                                                                          597
   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  (0, 0)

(no "SCOP Domain" information available for 2GL9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GL9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GL9)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (ASPG_ELIMR | Q47898)
molecular function
    GO:0003948    N4-(beta-N-acetylglucosaminyl)-L-asparaginase activity    Catalysis of the reaction: N(4)-(beta-N-acetyl-D-glucosaminyl)-L-asparagine + H(2)O = N-acetyl-beta-D-glucosaminylamine + L-aspartate + H(+).
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

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 Related Entries

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

UniProtKB/Swiss-Prot
        ASPG_ELIMR | Q47898: 1ayy 1p4k 1p4v 2gac 2gaw 3ljq 4r4y 9gaa 9gac 9gaf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2GL9)