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(-) Description

Title :  CRYSTAL STRUCTURE OF POTASSIUM-DEPENDENT PLANT-TYPE L-ASPARAGINASE FROM PHASEOLUS VULGARIS IN COMPLEX WITH K+ CATIONS
 
Authors :  M. Bejger, M. Gilski, B. Imiolczyk, M. Jaskolski
Date :  12 Mar 14  (Deposition) - 03 Sep 14  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Metal Binding Sites, Potassium Coordination, K-Dependent Enzyme, Ntn- Hydrolase, Plant Protein, L-Asparaginase, Isoaspartyl Aminopeptidase, Amidohydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bejger, B. Imiolczyk, D. Clavel, M. Gilski, A. Pajak, F. Marsolais, M. Jaskolski
Na+/K+ Exchange Switches The Catalytic Apparatus Of Potassium-Dependent Plant L-Asparaginase
Acta Crystallogr. , Sect. D V. 70 1854 2014
PubMed-ID: 25004963  |  Reference-DOI: 10.1107/S1399004714008700
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-ASPARAGINASE ALPHA SUBUNIT
    Chains: A, C
    EC Number: 3.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL SUBUNIT ALPHA (UNP RESIDUES 1-195)
    Gene: PHAVU_001G025000G
    Organism Common: FRENCH BEAN,KIDNEY BEAN,STRING BEAN
    Organism Scientific: PHASEOLUS VULGARIS
    Organism Taxid: 3885
    Synonym: L-ASPARAGINE AMIDOHYDROLASE
 
Molecule 2 - L-ASPARAGINASE BETA SUBUNIT
    Chains: B, D
    EC Number: 3.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL SUBUNIT BETA (UNP RESIDUES 196-326)
    Gene: PHAVU_001G025000G
    Organism Common: FRENCH BEAN,KIDNEY BEAN,STRING BEAN
    Organism Scientific: PHASEOLUS VULGARIS
    Organism Taxid: 3885
    Other Details: SUBUNITS ALPHA (CHAINS A, C) AND BETA (CHAINS B, D) ARE, RESPECTIVELY, THE N- AND C-TERMINAL PRODUCTS OF AUTOPROTEOLYTIC CLEAVAGE OF A PRECURSOR.
    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
1ASP1Mod. Amino AcidASPARTIC ACID
2K4Ligand/IonPOTASSIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:58 , GLU A:59 , ASP A:61 , PHE A:64 , SER A:66 , ARG A:68BINDING SITE FOR RESIDUE K A 201
2AC2SOFTWAREVAL A:111 , MET A:112 , SER A:115 , HIS A:117 , HOH A:305 , HOH A:338BINDING SITE FOR RESIDUE K A 202
3AC3SOFTWARETHR B:196 , GLY B:216 , ARG B:224 , ASP B:227 , THR B:246 , GLY B:247 , GLY B:249 , HOH B:604 , HOH B:605 , HOH B:622BINDING SITE FOR RESIDUE ASP B 501
4AC4SOFTWARELEU C:58 , GLU C:59 , ASP C:61 , PHE C:64 , SER C:66 , ARG C:68BINDING SITE FOR RESIDUE K C 201
5AC5SOFTWAREVAL C:111 , MET C:112 , SER C:115 , HIS C:117 , HOH C:309BINDING SITE FOR RESIDUE K C 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PU6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PU6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PU6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PU6)

(-) Exons   (0, 0)

(no "Exon" information available for 4PU6)

(-) 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:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.hhheeeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pu6 A   2 GGWAIAVHGGAGVDPTLPLERQEEAKQLLTRCLNLGISALNSNVPAIDVVELVVRELETDPLFNSGRGSALTEKGTVEMEASIMDGPKRRCGAVSGLTTVKNPISLARLVMDKSPHSYIAFSGAEDFARQQGVEVVDNEYFVTPDNVGMLKLAKEAN 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain B from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee....................eee...eeeeeeehhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.....eeeeeee....eeeee....eeeeeee....eeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pu6 B 196 TVGCVVVDREGRCAAATSTGGLMNKMTGRIGDSPLIGAGTYACDVCGVSCTGEGEAIIRGTLAREVAAVMEYKGLKLHQAVDFVIKHRLDEGKAGLIAVSNTGEVACGFNCNGMFRACATEDGFMEVAIWDD 501
                                   205       215       225       235       245       255       265       275       285       295       305       315       325||
                                                                                                                                                            326|
                                                                                                                                                             501


Chain C from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee....eeeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pu6 C   2 GGWAIAVHGGAGVDPTLPLERQEEAKQLLTRCLNLGISALNSNVPAIDVVELVVRELETDPLFNSGRGSALTEKGTVEMEASIMDGPKRRCGAVSGLTTVKNPISLARLVMDKSPHSYIAFSGAEDFARQQGVEVVDNEYFVTPDNVGMLKLAKEAN 158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       


Chain D from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeeee....................eee...eeeeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh......eeeeeee....eeeee....eeeeee.....eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pu6 D 196 TVGCVVVDREGRCAAATSTGGLMNKMTGRIGDSPLIGAGTYACDVCGVSCTGEGEAIIRGTLAREVAAVMEYKGLKLHQAVDFVIKHRLDEGKAGLIAVSNTGEVACGFNCNGMFRACATEDGFMEVAIWD 326
                                   205       215       225       235       245       255       265       275       285       295       305       315       325
   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 4PU6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PU6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PU6)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        V7CU13_PHAVU | V7CU13: 4pv2 4pv3

(-) Related Entries Specified in the PDB File

1jn9 ESCHERICHIA COLI L-ASPARAGINASE (ECAIII)
1k2x ESCHERICHIA COLI L-ASPARAGINASE (ECAIII)
1t3m ESCHERICHIA COLI L-ASPARAGINASE (ECAIII)
2gez LUPINUS LUTEUS L-ASPARAGINASE (LLA)
2zak ESCHERICHIA COLI L-ASPARAGINASE MUTANT (ECAIII T179A)
2zal ESCHERICHIA COLI L-ASPARAGINASE (ECAIII)
3c17 ESCHERICHIA COLI L-ASPARAGINASE MUTANT (ECAIII T179A)
4gdt HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4gdu HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4gdv HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4gdw HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4hlo HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4hlp HUMAN ASPARAGINASE-LIKE PROTEIN (HASNASE3)
4pv2 CRYSTAL STRUCTURE OF POTASSIUM-DEPENDENT PLANT-TYPE L- ASPARAGINASE FROM PHASEOLUS VULGARIS IN COMPLEX WITH K+ AND NA+ CATIONS
4pv3 CRYSTAL STRUCTURE OF POTASSIUM-DEPENDENT PLANT-TYPE L- ASPARAGINASE FROM PHASEOLUS VULGARIS IN COMPLEX WITH NA+ CATIONS