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(-) Description

Title :  CRYSTAL STRUCTURE OF POTASSIUM-INDEPENDENT PLANT ASPARAGINASE
 
Authors :  K. Michalska, G. Bujacz, M. Jaskolski
Date :  21 Mar 06  (Deposition) - 25 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Isoaspartyl Aminopeptidase, L-Asparaginase, Ntn-Hydrolase, Autoproteolysis, Taspase, Sodium Binding, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Michalska, G. Bujacz, M. Jaskolski
Crystal Structure Of Plant Asparaginase.
J. Mol. Biol. V. 360 105 2006
PubMed-ID: 16725155  |  Reference-DOI: 10.1016/J.JMB.2006.04.066
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-ASPARAGINASE ALPHA SUBUNIT
    Chains: A, C, E, G
    EC Number: 3.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 CODON PLUS RIP
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL SUBUNIT (RESIDUES 1-192)
    Organism Common: YELLOW LUPINE
    Organism Scientific: LUPINUS LUTEUS
    Organism Taxid: 3873
    Strain: CV. VENTUS
    Synonym: L-ASPARAGINE AMIDOHYDROLASE
 
Molecule 2 - L-ASPARAGINASE BETA SUBUNIT
    Chains: B, D, F, H
    EC Number: 3.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21 CODON PLUS RIP
    Expression System Taxid: 562
    Expression System Vector Type: PLASIMD
    Fragment: C-TERMINAL SUBUNIT (RESIDUES 193-325)
    Organism Common: YELLOW LUPINE
    Organism Scientific: LUPINUS LUTEUS
    Organism Taxid: 3873
    Other Details: SUBUNITS ALPHA (CHAINS A, C, E, G) AND BETA (CHAINS B, D, F, H) ARE, RESPECTIVELY, THE N- AND C-TERMINAL PRODUCTS OF AUTOPROTEOLYTIC CLEAVAGE OF A PRECURSOR
    Strain: CV. VENTUS
    Synonym: L-ASPARAGINE AMIDOHYDROLASE

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2NA4Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2NA-1Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:59 , GLU A:60 , ILE A:62 , PHE A:65 , ALA A:67 , ILE A:69BINDING SITE FOR RESIDUE NA A 401
02AC2SOFTWAREGLY B:213 , ARG B:221BINDING SITE FOR RESIDUE CL B 406
03AC3SOFTWARELEU C:59 , GLU C:60 , ILE C:62 , PHE C:65 , ALA C:67 , ILE C:69BINDING SITE FOR RESIDUE NA C 400
04AC4SOFTWAREILE D:321 , TRP D:322BINDING SITE FOR RESIDUE CL D 405
05AC5SOFTWARELEU D:214 , ARG D:221 , GLY D:246BINDING SITE FOR RESIDUE CL D 407
06AC6SOFTWARELEU E:59 , GLU E:60 , ILE E:62 , PHE E:65 , ALA E:67 , ILE E:69BINDING SITE FOR RESIDUE NA E 402
07AC7SOFTWAREILE F:321 , TRP F:322BINDING SITE FOR RESIDUE CL F 404
08AC8SOFTWAREARG F:221 , GLY F:246BINDING SITE FOR RESIDUE CL F 408
09AC9SOFTWAREGLU G:60 , ILE G:62 , PHE G:65 , ALA G:67 , ILE G:69BINDING SITE FOR RESIDUE NA G 403
10BC1SOFTWARELEU H:214 , ARG H:221BINDING SITE FOR RESIDUE CL H 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2GEZ)

(-) Sequences/Alignments

Asymmetric 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:158
 aligned with ASPG_LUPLU | Q9ZSD6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           ASPG_LUPLU     2 GGWSIALHGGAGDIPFSLPPERRKPREEGLRHCLQIGVEALKAQKPPLDVVELVVRELENIEHFNAGIGSVLTNSGTVEMEASIMDGNTMKCGAVSGLSTVLNPISLARLVMDKTPHIYLAFQGAQDFAKQQGVETVDSSHLITAENVERLKLAIEAN 159
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee....eeeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gez A   2 GGWSIALHGGAGDIPFSLPPERRKPREEGLRHCLQIGVEALKAQKPPLDVVELVVRELENIEHFNAGIGSVLTNSGTVEMEASIMDGNTMKCGAVSGLSTVLNPISLARLVMDKTPHIYLAFQGAQDFAKQQGVETVDSSHLITAENVERLKLAIEAN 159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        


Chain B from PDB  Type:PROTEIN  Length:133
 aligned with ASPG_LUPLU | Q9ZSD6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:133
                                   202       212       222       232       242       252       262       272       282       292       302       312       322   
           ASPG_LUPLU   193 TVGCVAVDSHGNLASATSTGGLVNKMVGRIGDTPLIGAGTYANELCAVSATGKGEEIIRATVARDVAALMEFKGLSLKEAADFVIHERTPKGTVGLIAVSAAGEIAMPFNTTGMFRACATEDGYSEIAIWPTT 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee.........ee.........eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh......eeeeeee....ee......eeeeeeee....eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gez B 193 TVGCVAVDSHGNLASATSTGGLVNKMVGRIGDTPLIGAGTYANELCAVSATGKGEEIIRATVARDVAALMEFKGLSLKEAADFVIHERTPKGTVGLIAVSAAGEIAMPFNTTGMFRACATEDGYSEIAIWPTT 325
                                   202       212       222       232       242       252       262       272       282       292       302       312       322   


Chain C from PDB  Type:PROTEIN  Length:166
 aligned with ASPG_LUPLU | Q9ZSD6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:166
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      
           ASPG_LUPLU     2 GGWSIALHGGAGDIPFSLPPERRKPREEGLRHCLQIGVEALKAQKPPLDVVELVVRELENIEHFNAGIGSVLTNSGTVEMEASIMDGNTMKCGAVSGLSTVLNPISLARLVMDKTPHIYLAFQGAQDFAKQQGVETVDSSHLITAENVERLKLAIEANRVQVDYSQ 167
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...................eeeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gez C   2 GGWSIALHGGAGDIPFSLPPERRKPREEGLRHCLQIGVEALKAQKPPLDVVELVVRELENIEHFNAGIGSVLTNSGTVEMEASIMDGNTMKCGAVSGLSTVLNPISLARLVMDKTPHIYLAFQGAQDFAKQQGVETVDSSHLITAENVERLKLAIEANRVQVDYSQ 167
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161      


Chain D from PDB  Type:PROTEIN  Length:133
 aligned with ASPG_LUPLU | Q9ZSD6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:133
                                   202       212       222       232       242       252       262       272       282       292       302       312       322   
           ASPG_LUPLU   193 TVGCVAVDSHGNLASATSTGGLVNKMVGRIGDTPLIGAGTYANELCAVSATGKGEEIIRATVARDVAALMEFKGLSLKEAADFVIHERTPKGTVGLIAVSAAGEIAMPFNTTGMFRACATEDGYSEIAIWPTT 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee.........ee.........eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....eeeeeee....ee......eeeeeeee....eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gez D 193 TVGCVAVDSHGNLASATSTGGLVNKMVGRIGDTPLIGAGTYANELCAVSATGKGEEIIRATVARDVAALMEFKGLSLKEAADFVIHERTPKGTVGLIAVSAAGEIAMPFNTTGMFRACATEDGYSEIAIWPTT 325
                                   202       212       222       232       242       252       262       272       282       292       302       312       322   


Chain E from PDB  Type:PROTEIN  Length:165
 aligned with ASPG_LUPLU | Q9ZSD6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     
           ASPG_LUPLU     2 GGWSIALHGGAGDIPFSLPPERRKPREEGLRHCLQIGVEALKAQKPPLDVVELVVRELENIEHFNAGIGSVLTNSGTVEMEASIMDGNTMKCGAVSGLSTVLNPISLARLVMDKTPHIYLAFQGAQDFAKQQGVETVDSSHLITAENVERLKLAIEANRVQVDYS 166
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...................eeeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gez E   2 GGWSIALHGGAGDIPFSLPPERRKPREEGLRHCLQIGVEALKAQKPPLDVVELVVRELENIEHFNAGIGSVLTNSGTVEMEASIMDGNTMKCGAVSGLSTVLNPISLARLVMDKTPHIYLAFQGAQDFAKQQGVETVDSSHLITAENVERLKLAIEANRVQVDYS 166
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     


Chain F from PDB  Type:PROTEIN  Length:133
 aligned with ASPG_LUPLU | Q9ZSD6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:133
                                   202       212       222       232       242       252       262       272       282       292       302       312       322   
           ASPG_LUPLU   193 TVGCVAVDSHGNLASATSTGGLVNKMVGRIGDTPLIGAGTYANELCAVSATGKGEEIIRATVARDVAALMEFKGLSLKEAADFVIHERTPKGTVGLIAVSAAGEIAMPFNTTGMFRACATEDGYSEIAIWPTT 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee....................eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....eeeeeee....ee......eeeeeeee....eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gez F 193 TVGCVAVDSHGNLASATSTGGLVNKMVGRIGDTPLIGAGTYANELCAVSATGKGEEIIRATVARDVAALMEFKGLSLKEAADFVIHERTPKGTVGLIAVSAAGEIAMPFNTTGMFRACATEDGYSEIAIWPTT 325
                                   202       212       222       232       242       252       262       272       282       292       302       312       322   


Chain G from PDB  Type:PROTEIN  Length:158
 aligned with ASPG_LUPLU | Q9ZSD6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
           ASPG_LUPLU     2 GGWSIALHGGAGDIPFSLPPERRKPREEGLRHCLQIGVEALKAQKPPLDVVELVVRELENIEHFNAGIGSVLTNSGTVEMEASIMDGNTMKCGAVSGLSTVLNPISLARLVMDKTPHIYLAFQGAQDFAKQQGVETVDSSHLITAENVERLKLAIEAN 159
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.....eeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gez G   2 GGWSIALHGGAGDIPFSLPPERRKPREEGLRHCLQIGVEALKAQKPPLDVVELVVRELENIEHFNAGIGSVLTNSGTVEMEASIMDGNTMKCGAVSGLSTVLNPISLARLVMDKTPHIYLAFQGAQDFAKQQGVETVDSSHLITAENVERLKLAIEAN 159
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        


Chain H from PDB  Type:PROTEIN  Length:133
 aligned with ASPG_LUPLU | Q9ZSD6 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:133
                                   202       212       222       232       242       252       262       272       282       292       302       312       322   
           ASPG_LUPLU   193 TVGCVAVDSHGNLASATSTGGLVNKMVGRIGDTPLIGAGTYANELCAVSATGKGEEIIRATVARDVAALMEFKGLSLKEAADFVIHERTPKGTVGLIAVSAAGEIAMPFNTTGMFRACATEDGYSEIAIWPTT 325
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee.........ee.........eee...eeeeeeehhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....eeeeeee....ee......eeeeeeee....eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gez H 193 TVGCVAVDSHGNLASATSTGGLVNKMVGRIGDTPLIGAGTYANELCAVSATGKGEEIIRATVARDVAALMEFKGLSLKEAADFVIHERTPKGTVGLIAVSAAGEIAMPFNTTGMFRACATEDGYSEIAIWPTT 325
                                   202       212       222       232       242       252       262       272       282       292       302       312       322
   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 2GEZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (ASPG_LUPLU | Q9ZSD6)
molecular function
    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: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)

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(-) Related Entries Specified in the PDB File

1apy HUMAN ASPARTYLGLUCOSAMINIDASE
1jn9 STRUCTURE OF PUTATIVE ASPARAGINASE ENCODED BY ESCHERICHIA COLI YBIK GENE
1k2x STRUCTURE OF PUTATIVE ASPARAGINASE ENCODED BY ESCHERICHIA COLI YBIK GENE
1seo CRYSTAL STRUCTURE OF E. COLI ISOASPARTYL AMINOPEPTIDASE IN COMPLEX WITH L-ASPARTATE
1t3m STRUCTURE OF THE ISOASPARTYL PEPTIDASE WITH L-ASPARAGINASE ACTIVITY FROM E. COLI
2a8j CRYSTAL STRUCTURE OF HUMAN TASPASE1 (ACIVATED FORM)
2gaw WILD TYPE GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM