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(-) Description

Title :  CRYSTAL STRUCTURE OF E. COLI ISOASPARTYL AMINOPEPTIDASE/L-ASPARAGINASE IN COMPLEX WITH L-ASPARTATE
 
Authors :  K. Michalska, K. Brzezinski, M. Jaskolski
Date :  07 Oct 07  (Deposition) - 30 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Isoaspartyl Peptidase, Asparaginase, Ntn-Hydrolase, Autoproteolysis, L-Aspartate/Calcium Cluster, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Michalska, K. Brzezinski, M. Jaskolski
Crystal Structure Of Isoaspartyl Aminopeptidase In Complex With L-Aspartate
J. Biol. Chem. V. 280 28484 2005
PubMed-ID: 15946951  |  Reference-DOI: 10.1074/JBC.M504501200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-ASPARAGINASE
    ChainsA, C
    EC Number3.4.19.5, 3.5.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11D
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentN-TERMINAL SUBUNIT (ALPHA), UNP RESIDUES 2-161
    GeneYBIK (IAAA)
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    Other DetailsTHE N-TERMINAL METHIONINE HAS BEEN REMOVED BY AN INTRACELLULAR AMINOPEPTIDASE (E. COLI). DURING EXPRESSION AND PURIFICATION, THE PROTEIN UNDERGOES AUTOPROTEOLYTIC CLEAVAGE INTO ALPHA AND BETA SUBUNITS. THE RESIDUES 162-178 WERE NOT PRESENT IN THE CRYSTALLIZED MATERIAL DUE TO PARTIAL, NON-SPECIFIC DEGRADATION AT THE C-TERMINUS. THE NUMBER OF MISSING RESIDUES WAS DETERMINED BY MASS SPECTROMETRY
    StrainK12
    SynonymL-ASPARAGINASE SUBUNIT ALPHA, L-ASPARAGINE AMIDOHYDROLASE
 
Molecule 2 - L-ASPARAGINASE
    ChainsB, D
    EC Number3.4.19.5, 3.5.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11D
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL SUBUNIT (BETA), UNP RESIDUES 179-315
    GeneYBIK (IAAA)
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    Other DetailsDURING EXPRESSION AND PURIFICATION, THE PROTEIN UNDERGOES AUTOPROTEOLYTIC CLEAVAGE INTO ALPHA AND BETA SUBUNITS. THE RESIDUES 316-321 WERE NOT PRESENT IN THE CRYSTALLIZED MATERIAL DUE TO PARTIAL, NON-SPECIFIC DEGRADATION AT THE C-TERMINUS. THE NUMBER OF MISSING RESIDUES WAS DETERMINED BY MASS SPECTROMETRY
    StrainK12
    SynonymL-ASPARAGINASE SUBUNIT BETA, L-ASPARAGINE AMIDOHYDROLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1ASP5Mod. Amino AcidASPARTIC ACID
2CA5Ligand/IonCALCIUM ION
3CL1Ligand/IonCHLORIDE ION
4NA2Ligand/IonSODIUM ION
5TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (0, 0)

(no "Site" information available for 2ZAL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZAL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZAL)

(-) 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:161
 aligned with IAAA_ECOLI | P37595 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
           IAAA_ECOLI     2 GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGATVLD 165
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh---. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zal A   2 GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAARKEGA---D 503
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161   |
                                                                                                                                                                                         161 503

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with IAAA_ECOLI | P37595 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:138
                                   188       198       208       218       228       238       248       258       268       278       288       298       308        
           IAAA_ECOLI   179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYREKGD 316
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee.........ee.........eee....eeeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...eeeeeee....ee......eeeeeeee.....eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zal B 179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYREDDD 504
                                   188       198       208       218       228       238       248       258       268       278       288       298       308    ||||
                                                                                                                                                                313|||
                                                                                                                                                                 501||
                                                                                                                                                                  502|
                                                                                                                                                                   504

Chain C from PDB  Type:PROTEIN  Length:156
 aligned with IAAA_ECOLI | P37595 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
           IAAA_ECOLI     2 GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAAR 157
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2zal C   2 GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAAR 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      

Chain D from PDB  Type:PROTEIN  Length:136
 aligned with IAAA_ECOLI | P37595 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:136
                                   188       198       208       218       228       238       248       258       268       278       288       298       308      
           IAAA_ECOLI   179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYREK 314
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Asparaginase_2-2zalD01 D:179-500                                                                                                         Pfam domains (1)
           Pfam domains (2) Asparaginase_2-2zalD02 D:179-500                                                                                                         Pfam domains (2)
           Pfam domains (3) Asparaginase_2-2zalD03 D:179-500                                                                                                         Pfam domains (3)
           Pfam domains (4) Asparaginase_2-2zalD04 D:179-500                                                                                                         Pfam domains (4)
         Sec.struct. author .eeeeee.....eeeeeee.........ee.........eee....eeeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...eeeeeee....ee......eeeeeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zal D 179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYRED 500
                                   188       198       208       218       228       238       248       258       268       278       288       298       308    ||
                                                                                                                                                                313|
                                                                                                                                                                 500

   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 2ZAL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (IAAA_ECOLI | P37595)
molecular function
    GO:0004067    asparaginase activity    Catalysis of the reaction: L-asparagine + H2O = L-aspartate + NH3.
    GO:0008798    beta-aspartyl-peptidase activity    Catalysis of the cleavage of a beta-linked aspartic residue from the N-terminus of a polypeptide.
    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:0016540    protein autoprocessing    Processing which a protein carries out itself. This involves actions such as the autolytic removal of residues to generate the mature form of the protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IAAA_ECOLI | P375951jn9 1k2x 1t3m 2zak 3c17

(-) Related Entries Specified in the PDB File

1apy HUMAN ASPARTYLGLUCOSAMINIDASE
1apz HUMAN ASPARTYLGLUCOSAMINIDASE COMPLEX WITH REACTION PRODUCT
1ayy GLYCOSYLASPARAGINASE
1jn9 STRUCTURE OF PUTATIVE ASPARAGINASE ENCODED BY ESCHERICHIA COLI YBIK GENE
1k2x STRUCTURE OF PUTATIVE ASPARAGINASE ENCODED BY ESCHERICHIA COLI YBIK GENE
1p4v CRYSTAL STRUCTURE OF THE GLYCOSYLASPARAGINASE PRECURSOR D151N MUTANT WITH GLYCINE
1t3m STRUCTURE OF THE ISOASPARTYL PEPTIDASE WITH L-ASPARAGINASE ACTIVITY FROM E. COLI
2gac T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
2gaw WILD TYPE GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
9gaa PRECURSOR OF T152A THE GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM T152A MUTANT
9gac PRECURSOR OF THE T152C MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
9gaf PRECURSOR OF THE W11F MUTANT GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM