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(-) Description

Title :  CRYSTAL STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINASE COMPLEXED WITH 6-HYDROXY-D-NORLEUCINE
 
Authors :  K. Aghaiypour, A. Wlodawer, J. Lubkowski
Date :  17 Aug 01  (Deposition) - 09 Jan 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  L-Asparaginase, Amidohydrolase, Bacteria, Covalent Complex, Suicide Inhibitor, Don, Enzyme, Active Site, Tetramer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Aghaiypour, A. Wlodawer, J. Lubkowski
Do Bacterial L-Asparaginases Utilize A Catalytic Triad Thr-Tyr-Glu?
Biochim. Biophys. Acta V. 1550 117 2001
PubMed-ID: 11755201  |  Reference-DOI: 10.1016/S0167-4838(01)00270-9
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-ASPARAGINASE
    ChainsA, B, C, D
    EC Number3.5.1.1
    Organism ScientificERWINIA CHRYSANTHEMI
    Organism Taxid556

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2DDO4Ligand/Ion6-HYDROXY-D-NORLEUCINE
3GOL3Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , THR A:15 , TYR A:29 , ALA A:61 , SER A:62 , GLU A:63 , GLY A:94 , THR A:95 , ASP A:96 , ALA A:120 , MET A:121 , HOH A:2502 , HOH A:2506 , HOH A:2508 , HOH A:2510BINDING SITE FOR RESIDUE DDO A 2401
2AC2SOFTWAREGLY B:14 , THR B:15 , TYR B:29 , ALA B:61 , SER B:62 , GLU B:63 , GLY B:94 , THR B:95 , ASP B:96 , ALA B:120 , MET B:121 , HOH B:2403 , HOH B:2408 , HOH D:2604BINDING SITE FOR RESIDUE DDO B 2402
3AC3SOFTWARESER A:254 , HOH A:2740 , GLY C:14 , THR C:15 , TYR C:29 , ALA C:61 , SER C:62 , GLU C:63 , GLY C:94 , THR C:95 , ASP C:96 , ALA C:120 , MET C:121 , HOH C:2605 , HOH C:2609BINDING SITE FOR RESIDUE DDO C 2403
4AC4SOFTWARESER B:254 , HOH B:2635 , GLY D:14 , THR D:15 , TYR D:29 , ALA D:61 , SER D:62 , GLU D:63 , GLY D:94 , THR D:95 , ASP D:96 , ALA D:120 , MET D:121 , HOH D:2609 , HOH D:2613 , HOH D:2615BINDING SITE FOR RESIDUE DDO D 2404
5AC5SOFTWAREGLY A:241 , LYS A:243 , HOH A:2628 , HOH A:2690 , ASP C:210 , ARG C:212 , THR C:312BINDING SITE FOR RESIDUE 1PE A 2501
6AC6SOFTWAREASP A:68 , SER A:216 , LEU A:217 , LYS A:219 , MET A:308 , HOH A:2574 , THR C:215 , HOH C:2604 , HOH C:2624BINDING SITE FOR RESIDUE GOL C 2601
7AC7SOFTWARELEU B:267 , PRO B:291 , GLY B:292 , PRO B:317 , HOH B:2444 , HOH B:2637 , ARG D:313 , THR D:314 , SER D:315 , ASP D:316 , HOH D:2607BINDING SITE FOR RESIDUE GOL D 2602
8AC8SOFTWAREALA C:82 , ARG C:83 , ASP C:84 , ASP C:85BINDING SITE FOR RESIDUE GOL C 2603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 16)

Asymmetric/Biological Unit (4, 16)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_ASPG_DICCH_001 *L177IASPG_DICCH  ---  ---A/B/C/DI156I
2UniProtVAR_ASPG_DICCH_002 *K199RASPG_DICCH  ---  ---A/B/C/DR178R
3UniProtVAR_ASPG_DICCH_003 *M288LASPG_DICCH  ---  ---A/B/C/DL267L
4UniProtVAR_ASPG_DICCH_004 *I295MASPG_DICCH  ---  ---A/B/C/DM274M
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (3, 12)

Asymmetric/Biological Unit (3, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ASN_GLN_ASE_3PS51732 Asparaginase / glutaminase domain profile.ASPG_DICCH26-348
 
 
 
  4A:5-327
B:5-327
C:5-327
D:5-327
2ASN_GLN_ASE_1PS00144 Asparaginase / glutaminase active site signature 1.ASPG_DICCH30-38
 
 
 
  4A:9-17
B:9-17
C:9-17
D:9-17
3ASN_GLN_ASE_2PS00917 Asparaginase / glutaminase active site signature 2.ASPG_DICCH109-119
 
 
 
  4A:88-98
B:88-98
C:88-98
D:88-98

(-) Exons   (0, 0)

(no "Exon" information available for 1JSL)

(-) 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:324
 aligned with ASPG_DICCH | P06608 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:324
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344    
           ASPG_DICCH    25 LPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVLNDRIGSARYITKTNASTLDTFKANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKAMEKGVVVIRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY 348
               SCOP domains d1jsla_ A: Asparaginase type II                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jslA01 A:4-218  [code=3.40.50.1170, no name defined]                                                                                                                                                                  1jslA02 A:219-327  [code=3.40.50.40, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.hhhh................hhhhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhhhhhhhh....eeee..eeee....ee........ee.......eeee..eeee.eee...hhhhh............eeeee......hhhhhhhhhh...eeeeee......hhhhhhhhhhhhhh..eeeeee...............ee....hhhhhhhhhhhhh....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------I---------------------R----------------------------------------------------------------------------------------L------M----------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ASN_GLN_ASE_3  PDB: A:5-327 UniProt: 26-348                                                                                                                                                                                                                                                                                         PROSITE (1)
                PROSITE (2) -----ASN_GLN_A----------------------------------------------------------------------ASN_GLN_ASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jsl A   4 LPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVINDRIGSARYITKTNASTLDTFRANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKALEKGVVVMRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY 327
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323    

Chain B from PDB  Type:PROTEIN  Length:324
 aligned with ASPG_DICCH | P06608 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:324
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344    
           ASPG_DICCH    25 LPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVLNDRIGSARYITKTNASTLDTFKANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKAMEKGVVVIRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY 348
               SCOP domains d1jslb_ B: Asparaginase type II                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jslB01 B:4-218  [code=3.40.50.1170, no name defined]                                                                                                                                                                  1jslB02 B:219-327  [code=3.40.50.40, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.hhhh................hhhhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhhhhhhhh....eeee..eeee....ee........ee.......eeee..eeee.eee...hhhhh............eeeee......hhhhhhhhhh...eeeeee......hhhhhhhhhhhhhh..eeeeee...............ee....hhhhhhhhhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------I---------------------R----------------------------------------------------------------------------------------L------M----------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ASN_GLN_ASE_3  PDB: B:5-327 UniProt: 26-348                                                                                                                                                                                                                                                                                         PROSITE (1)
                PROSITE (2) -----ASN_GLN_A----------------------------------------------------------------------ASN_GLN_ASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jsl B   4 LPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVINDRIGSARYITKTNASTLDTFRANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKALEKGVVVMRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY 327
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323    

Chain C from PDB  Type:PROTEIN  Length:324
 aligned with ASPG_DICCH | P06608 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:324
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344    
           ASPG_DICCH    25 LPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVLNDRIGSARYITKTNASTLDTFKANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKAMEKGVVVIRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY 348
               SCOP domains d1jslc_ C: Asparaginase type II                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jslC01 C:4-218  [code=3.40.50.1170, no name defined]                                                                                                                                                                  1jslC02 C:219-327  [code=3.40.50.40, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.hhhh................hhhhhhhhh.hhhhhheeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhhhhhhhh....eeee..eeee....ee........ee.......eeee..eeee.eee...hhhhh............eeeee......hhhhhhhhhh...eeeeee......hhhhhhhhhhhhhh..eeeeee...............ee....hhhhhhhhhhhhh....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------I---------------------R----------------------------------------------------------------------------------------L------M----------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ASN_GLN_ASE_3  PDB: C:5-327 UniProt: 26-348                                                                                                                                                                                                                                                                                         PROSITE (1)
                PROSITE (2) -----ASN_GLN_A----------------------------------------------------------------------ASN_GLN_ASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jsl C   4 LPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVINDRIGSARYITKTNASTLDTFRANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKALEKGVVVMRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY 327
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323    

Chain D from PDB  Type:PROTEIN  Length:324
 aligned with ASPG_DICCH | P06608 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:324
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344    
           ASPG_DICCH    25 LPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVLNDRIGSARYITKTNASTLDTFKANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKAMEKGVVVIRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY 348
               SCOP domains d1jsld_ D: Asparaginase type II                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1jslD01 D:4-218  [code=3.40.50.1170, no name defined]                                                                                                                                                                  1jslD02 D:219-327  [code=3.40.50.40, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee.hhhh................hhhhhhhhhhhhhhh.eeeeeeeeeehhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhhh.....eeee...........hhhhhhhhhhhhhhhhhhh....eeee..eeee....ee........ee.......eeee..eeee.eee...hhhhh............eeeee......hhhhhhhhhh...eeeeee......hhhhhhhhhhhhhh..eeeeee...............ee....hhhhhhhhhhhhh....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------I---------------------R----------------------------------------------------------------------------------------L------M----------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -ASN_GLN_ASE_3  PDB: D:5-327 UniProt: 26-348                                                                                                                                                                                                                                                                                         PROSITE (1)
                PROSITE (2) -----ASN_GLN_A----------------------------------------------------------------------ASN_GLN_ASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jsl D   4 LPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVINDRIGSARYITKTNASTLDTFRANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKALEKGVVVMRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY 327
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323    

   Legend:   → Mismatch (orange background)
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    → 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, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1JSL)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (ASPG_DICCH | P06608)
molecular function
    GO:0004067    asparaginase activity    Catalysis of the reaction: L-asparagine + H2O = L-aspartate + NH3.
    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.
biological process
    GO:0006528    asparagine metabolic process    The chemical reactions and pathways involving asparagine, 2-amino-3-carbamoylpropanoic acid.
    GO:0006520    cellular amino acid metabolic process    The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ASPG_DICCH | P066081hfj 1hfk 1hfw 1hg0 1hg1 1jsr 1o7j 5f52 5hw0 5i3z 5i48 5i4b

(-) Related Entries Specified in the PDB File

1hfw X-RAY STRUCTURE OF THE COMPLEX BETWEEN ERWINIA CHRYSANTHEMI L-ASPARAGINASE AND L-GLUTAMATE
1hg0 X-RAY STRUCTURE OF THE COMPLEX BETWEEN ERWINIA CHRYSANTHEMI L-ASPARAGINASE AND SUCCINIC ACID
1hg1 X-RAY STRUCTURE OF THE COMPLEX BETWEEN ERWINIA CHRYSANTHEMI L-ASPARAGINASE AND D-ASPARTATE
1jsr CRYSTAL STRUCTURE OF ERWINIA CHRYSANTHEMI L-ASPARAGINASE COMPLEXED WITH 6-HYDROXY-L-NORLEUCINE