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(-) Description

Title :  X-RAY STRUCTURE OF THE COMPLEX BETWEEN ERWINIA CHRYSANTHEMI L-ASPARAGINASE AND L-GLUTAMATE
 
Authors :  J. Lubkowski, A. Wlodawer, K. A. Kolyani
Date :  08 Dec 00  (Deposition) - 07 Aug 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Asparaginase, Hydrolase, X-Ray, Structure, Complex, D- Aspartate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Kolyani, A. Wlodawer, J. Lubkowski
Stuctural Basis For The Activity And Substrate Specificity Of Erwinia Chrysanthemi L-Asparaginase
Biochemistry V. 40 5655 2001
PubMed-ID: 11341830  |  Reference-DOI: 10.1021/BI0029595
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-ASPARAGINASE
    Chains: A, B, C, D
    EC Number: 3.5.1.1
    Organism Scientific: ERWINIA CHRYSANTHEMI
    Organism Taxid: 556
    Other Details: THE NEW NAME OF ERWINIA CHRYSANTHEMI IS PECTOBACTERIUM CHRYSANTHEMI
    Strain: NCPPB 1125
    Synonym: L-ASPARAGINE AMIDOHYDROLASE, L-ASNASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1GLU4Mod. Amino AcidGLUTAMIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:14 , THR A:15 , ALA A:61 , SER A:62 , GLU A:63 , GLY A:94 , THR A:95 , ASP A:96 , ALA A:120 , HOH A:2215 , HOH A:2216 , SER C:254BINDING SITE FOR RESIDUE GLU A 350
2AC2SOFTWAREGLY B:14 , THR B:15 , ALA B:61 , SER B:62 , GLU B:63 , GLY B:94 , THR B:95 , ASP B:96 , HOH B:2249 , HOH B:2250 , HOH B:2251 , SER D:254BINDING SITE FOR RESIDUE GLU B 350
3AC3SOFTWARESER A:254 , GLY C:14 , THR C:15 , ALA C:61 , SER C:62 , GLU C:63 , GLY C:94 , THR C:95 , ASP C:96 , ALA C:120 , HOH C:2022 , HOH C:2233 , HOH C:2235BINDING SITE FOR RESIDUE GLU C 350
4AC4SOFTWARESER B:254 , GLY D:14 , THR D:15 , ALA D:61 , SER D:62 , GLU D:63 , GLY D:94 , THR D:95 , ASP D:96 , HOH D:2257 , HOH D:2258 , HOH D:2259BINDING SITE FOR RESIDUE GLU D 350

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 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:9-16
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 1HFW)

(-) 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:308
 aligned with ASPG_DICCH | P06608 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:326
                                                                                                                                                                                                                                                                                                                                                              348 
                                    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       333       343    | 
           ASPG_DICCH    24 KLPNIVILATGGTIAGSAATGTQTTGYKAGALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVLNDRIGSARYITKTNASTLDTFKANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKAMEKGVVVIRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTY-   -
               SCOP domains d1hfwa_ A: Aspa                  raginase type II                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1hfwA01 A:3-218                    [code=3.40.50.1170, no name defined]                                                                                                                                                 1hfwA02 A:219-326  [code=3.40.50.40, no name defined]                                                       -- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee......------------------hhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhhhhh....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
                 1hfw A   3 KLPNIVILATGGTIA------------------VDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVINDRIGSARYITKTNASTLDTFRANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKALEKGVVVMRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTYE 350
                                    12    |    -         -   |    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322    ||
                                         17                 36                                                                                                                                                                                                                                                                                                327|
                                                                                                                                                                                                                                                                                                                                                               350


Chain B from PDB  Type:PROTEIN  Length:310
 aligned with ASPG_DICCH | P06608 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:325
                                                                                                                                                                                                                                                                                                                                                             348 
                                    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-   -
               SCOP domains d1hfwb_ B: Asp               araginase type II                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1hfwB01 B:4-21               8  [code=3.40.50.1170, no name defined]                                                                                                                                                   1hfwB02 B:219-326  [code=3.40.50.40, no name defined]                                                       -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......---------------..hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhhhh.....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: B:5-327 UniProt: 26-348                                                                                                                                                                                                                                                                                        - PROSITE (1)
                PROSITE (2) -----ASN_GLN_A----------------------------------------------------------------------ASN_GLN_ASE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1hfw B   4 LPNIVILATGGTIA---------------ALGVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVINDRIGSARYITKTNASTLDTFRANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKALEKGVVVMRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTYE 350
                                    13   |     -        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   ||
                                        17              33                                                                                                                                                                                                                                                                                                   327|
                                                                                                                                                                                                                                                                                                                                                              350


Chain C from PDB  Type:PROTEIN  Length:308
 aligned with ASPG_DICCH | P06608 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:325
                                                                                                                                                                                                                                                                                                                                                             348 
                                    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-   -
               SCOP domains d1hfwc_ C: Asp                 araginase type II                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1hfwC01 C:4-21                 8  [code=3.40.50.1170, no name defined]                                                                                                                                                 1hfwC02 C:219-326  [code=3.40.50.40, no name defined]                                                       -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......-----------------hhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhhhhhhhhhhh......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
                 1hfw C   4 LPNIVILATGGTIA-----------------GVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVINDRIGSARYITKTNASTLDTFRANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKALEKGVVVMRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTYE 350
                                    13   |     -         - |      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   ||
                                        17                35                                                                                                                                                                                                                                                                                                 327|
                                                                                                                                                                                                                                                                                                                                                              350


Chain D from PDB  Type:PROTEIN  Length:307
 aligned with ASPG_DICCH | P06608 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:325
                                                                                                                                                                                                                                                                                                                                                             348 
                                    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-   -
               SCOP domains d1hfwd_ D: As                  paraginase type II                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1hfwD01 D:4-2                  18  [code=3.40.50.1170, no name defined]                                                                                                                                                1hfwD02 D:219-326  [code=3.40.50.40, no name defined]                                                       -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...------------------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
                 1hfw D   4 LPNIVILATGGTI------------------GVDTLINAVPEVKKLANVKGEQFSNMASENMTGDVVLKLSQRVNELLARDDVDGVVITHGTDTVEESAYFLHLTVKSDKPVVFVAAMRPATAISADGPMNLLEAVRVAGDKQSRGRGVMVVINDRIGSARYITKTNASTLDTFRANEEGYLGVIIGNRIYYQNRIDKLHTTRSVFDVRGLTSLPKVDILYGYQDDPEYLYDAAIQHGVKGIVYAGMGAGSVSVRGIAGMRKALEKGVVVMRSTRTGNGIVPPDEELPGLVSDSLNPAHARILLMLALTRTSDPKVIQEYFHTYE 350
                                    13  |      -         - |      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   ||
                                       16                 35                                                                                                                                                                                                                                                                                                 327|
                                                                                                                                                                                                                                                                                                                                                              350
   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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (0, 0)

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

(-) 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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  1hfw
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  ASPG_DICCH | P06608
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 Related Entries

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

UniProtKB/Swiss-Prot
        ASPG_DICCH | P06608: 1hfj 1hfk 1hg0 1hg1 1jsl 1jsr 1o7j 5f52 5hw0 5i3z 5i48 5i4b

(-) Related Entries Specified in the PDB File

1hfj ASPARAGINASE FROM ERWINIA CHRYSANTHEMI, HEXAGONAL FORM WITH SULFATE
1hfk ASPARAGINASE FROM ERWINIA CHRYSANTHEMI, HEXAGONAL FORM WITH PARTIAL SULFATE
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