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(-) Description

Title :  STRUCTURE OF THE ISOASPARTYL PEPTIDASE WITH L-ASPARAGINASE ACTIVITY FROM E. COLI
 
Authors :  A. Prahl, M. Pazgier, M. Hejazi, W. Lockau, J. Lubkowski
Date :  27 Apr 04  (Deposition) - 13 Jul 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Type Iii L-Asparaginase, Plant-Type Asparaginase, Isoaspartyl Peptidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Prahl, M. Pazgier, M. Hejazi, W. Lockau, J. Lubkowski
Structure Of The Isoaspartyl Peptidase With L-Asparaginase Activity From Escherichia Coli.
Acta Crystallogr. , Sect. D V. 60 1173 2004
PubMed-ID: 15159592  |  Reference-DOI: 10.1107/S0907444904003403
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE L-ASPARAGINASE
    Chains: A, C
    EC Number: 3.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: N-TERMINAL RESIDUES 1-177
    Gene: YBIK, B0828
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: L-ASPARAGINE AMIDOHYDROLASE
 
Molecule 2 - PUTATIVE L-ASPARAGINASE
    Chains: B, D
    EC Number: 3.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: C-TERMINAL RESIDUES 178-320
    Gene: YBIK, B0828
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: L-ASPARAGINE AMIDOHYDROLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2NO33Ligand/IonNITRATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:59 , GLU A:60 , CYS A:62 , PHE A:65 , ALA A:67 , ILE A:69BINDING SITE FOR RESIDUE NA A 801
2AC2SOFTWARELEU C:59 , GLU C:60 , CYS C:62 , PHE C:65 , ALA C:67 , ILE C:69BINDING SITE FOR RESIDUE NA C 802
3AC3SOFTWARETHR B:178 , ARG B:206 , GLY B:208 , ASP B:209 , GLY B:230 , GLY B:232 , HOH B:906 , HOH B:911 , HOH B:913 , HOH B:994BINDING SITE FOR RESIDUE NO3 B 901
4AC4SOFTWAREHOH A:1009 , HOH A:1071 , HIS C:101 , ARG C:137 , VAL C:138 , HOH C:952 , HOH C:1033BINDING SITE FOR RESIDUE NO3 C 902
5AC5SOFTWAREARG A:75 , LEU B:203 , HIS C:118BINDING SITE FOR RESIDUE NO3 A 903

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T3M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1T3M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T3M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T3M)

(-) Exons   (0, 0)

(no "Exon" information available for 1T3M)

(-) 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: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 d1t3m.1 A:,B: Glycosylasparaginase (aspartylglucosaminidase, AGA)                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t3m A   1 GKAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAAR 156
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150      


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with IAAA_ECOLI | P37595 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:134
                                   188       198       208       218       228       238       248       258       268       278       288       298       308    
           IAAA_ECOLI   179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYR 312
               SCOP domains d1t3m.1 A:,B: Glycosylasparaginase (aspartylglucosaminidase, AGA)                                                                      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
                 1t3m B 178 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYR 311
                                   187       197       207       217       227       237       247       257       267       277       287       297       307    


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

    Alignment length:156
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152      
           IAAA_ECOLI     3 KAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAARK 158
               SCOP domains d1t3m.2 C:,D: Glycosylasparaginase (aspartylglucosaminidase, AGA)                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t3m C   2 KAVIAIHGGAGAISRAQMSLQQELRYIEALSAIVETGQKMLEAGESALDVVTEAVRLLEECPLFNAGIGAVFTRDETHELDACVMDGNTLKAGAVAGVSHLRNPVLAARLVMEQSPHVMMIGEGAENFAFARGMERVSPEIFSTSLRYEQLLAARK 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      


Chain D from PDB  Type:PROTEIN  Length:134
 aligned with IAAA_ECOLI | P37595 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:134
                                   188       198       208       218       228       238       248       258       268       278       288       298       308    
           IAAA_ECOLI   179 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYR 312
               SCOP domains d1t3m.2 C:,D: Glycosylasparaginase (aspartylglucosaminidase, AGA)                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Asparaginase_2-1t3mD01 D:178-311                                                                                                       Pfam domains (1)
           Pfam domains (2) Asparaginase_2-1t3mD02 D:178-311                                                                                                       Pfam domains (2)
           Pfam domains (3) Asparaginase_2-1t3mD03 D:178-311                                                                                                       Pfam domains (3)
           Pfam domains (4) Asparaginase_2-1t3mD04 D:178-311                                                                                                       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
                 1t3m D 178 TVGAVALDLDGNLAAATSTGGMTNKLPGRVGDSPLVGAGCYANNASVAVSCTGTGEVFIRALAAYDIAALMDYGGLSLAEACERVVMEKLPALGGSGGLIAIDHEGNVALPFNTEGMYRAWGYAGDTPTTGIYR 311
                                   187       197       207       217       227       237       247       257       267       277       287       297       307
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1T3M)

(-) 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 | P37595: 1jn9 1k2x 2zak 2zal 3c17

(-) Related Entries Specified in the PDB File

1jn9 THE SAME ENZYME
1k2x THE SAME ENZYME