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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLYCOSYLASPARAGINASE PRECURSOR D151N MUTANT WITH GLYCINE
 
Authors :  X. Qian, C. Guan, H. C. Guo
Date :  24 Apr 03  (Deposition) - 06 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Alpha Beta, Beta Alpha, Sandwich, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Qian, C. Guan, H. C. Guo
A Dual Role For An Aspartic Acid In Glycosylasparaginase Autoproteolysis.
Structure V. 11 997 2003
PubMed-ID: 12906830  |  Reference-DOI: 10.1016/S0969-2126(03)00150-3
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - N(4)-(BETA-N-ACETYLGLUCOSAMINYL)-L-ASPARAGINASE PRECURSOR
    Chains: A, C
    EC Number: 3.5.1.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-C2X
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: GLYCOSYLASPARAGINASE, ALPHA AND BETA CHAINS
    Mutation: YES
    Organism Scientific: ELIZABETHKINGIA MENINGOSEPTICA
    Organism Taxid: 238
    Synonym: GLYCOSYLASPARAGINASE, ASPARTYLGLUCOSAMINIDASE, N4- N- ACETYL-BETA-GLUCOSAMINYL, -L-ASPARAGINE AMIDASE, AGA

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GLY2Mod. Amino AcidGLYCINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:152 , GLY A:172 , MET A:173 , ARG A:180 , ASP A:183 , SER A:184 , GLY A:204 , GLY A:206 , HOH A:301BINDING SITE FOR RESIDUE GLY A 296
2AC2SOFTWAREHOH C:7 , HOH C:10 , THR C:452 , GLY C:472 , MET C:473 , ARG C:480 , ASP C:483 , SER C:484 , GLY C:504 , GLY C:506BINDING SITE FOR RESIDUE GLY C 596

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P4V)

(-) 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 1P4V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P4V)

(-) Exons   (0, 0)

(no "Exon" information available for 1P4V)

(-) 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:296
 aligned with ASPG_ELIMR | Q47898 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:296
                                                                                                                                                                                                                                                                                                                                340 
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335    | 
           ASPG_ELIMR    46 TTNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQYKPIVNIENHDTIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALK-   -
               SCOP domains d1p4va_ A: Glycosylasparaginase (aspartylglucosaminidase, AGA)                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...................eeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh........hhhhhhhhhhhhh...............eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeeee....eeeee......eeeee..eeeee..ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p4v A   1 TTNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQYKPIVNIENHNTIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALKG 296
                                    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    ||
                                                                                                                                                                                                                                                                                                                                295|
                                                                                                                                                                                                                                                                                                                                 296


Chain C from PDB  Type:PROTEIN  Length:296
 aligned with ASPG_ELIMR | Q47898 from UniProtKB/Swiss-Prot  Length:340

    Alignment length:296
                                                                                                                                                                                                                                                                                                                                340 
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335    | 
           ASPG_ELIMR    46 TTNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQYKPIVNIENHDTIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALK-   -
               SCOP domains d1p4vc_ C: Glycosylasparaginase (aspartylglucosaminidase, AGA)                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Asparaginase_2-1p4vC01 C:301-595                                                                                                                                                                                                                                                                       - Pfam domains (1)
           Pfam domains (2) Asparaginase_2-1p4vC02 C:301-595                                                                                                                                                                                                                                                                       - Pfam domains (2)
         Sec.struct. author .....eeeee..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...................eeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh........hhhhhhhhhhhhh...............eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh..hhhhh.eeeeeee....eeeee......eeeee..eeeee..ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p4v C 301 TTNKPIVLSTWNFGLHANVEAWKVLSKGGKALDAVEKGVRLVEDDPTERSVGYGGRPDRDGRVTLDACIMDENYNIGSVACMEHIKNPISVARAVMEKTPHVMLVGDGALEFALSQGFKKENLLTAESEKEWKEWLKTSQYKPIVNIENHNTIGMIALDAQGNLSGACTTSGMAYKMHGRVGDSPIIGAGLFVDNEIGAATATGHGEEVIRTVGTHLVVELMNQGRTPQQACKEAVERIVKIVNRRGKNLKDIQVGFIALNKKGEYGAYCIQDGFNFAVHDQKGNRLETPGFALKG 596
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590    ||
                                                                                                                                                                                                                                                                                                                                595|
                                                                                                                                                                                                                                                                                                                                 596
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1P4V)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: NTN (93)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (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 2gac 2gaw 2gl9 3ljq 4r4y 9gaa 9gac 9gaf

(-) Related Entries Specified in the PDB File

1p4k CRYSTAL STRUCTURE OF THE GLYCOSYLASPARAGINASE PRECURSOR D151N MUTANT