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(-) Description

Title :  CRYSTAL STRUCTURE OF L-ASPARAGINASE I FROM YERSINIA PESTIS
 
Authors :  Y. Kim, M. Gu, J. Hasseman, W. F. Anderson, A. Joachimiak
Date :  05 Jul 10  (Deposition) - 04 Aug 10  (Release) - 04 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B  (2x)
Keywords :  Alpha-Beta-Alpha Sandwich, Csgid, Structural Genomics, Structural Genomics Of Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Gu, J. Hasseman, W. F. Anderson, A. Joachimiak
Crystal Structure Of L-Asparaginase I From Yersinia Pestis
To Be Published 2010
PubMed: search

(-) Compounds

Molecule 1 - CYTOPLASMIC L-ASPARAGINASE I
    Chains: A, B
    EC Number: 3.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLSMID
    Gene: ANSA, Y2161, YPO2161, YP_1961
    Organism Scientific: YERSINIA PESTIS
    Organism Taxid: 214092
    Strain: CO92
    Synonym: L-ASPARAGINASE I

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): A 
Biological Unit 2 (2x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 22)

Asymmetric Unit (2, 22)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 22)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE18Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 22)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE18Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:175 , ASN A:176 , THR A:271 , CYS A:273 , ILE A:274 , ASP A:299 , MSE A:300 , THR A:301 , VAL A:302 , HOH A:447 , HOH A:475 , HOH A:494 , HOH A:501BINDING SITE FOR RESIDUE GOL A 341
2AC2SOFTWAREGLN A:232 , ILE A:265 , HOH A:432BINDING SITE FOR RESIDUE GOL A 343
3AC3SOFTWAREGLN B:232 , VAL B:234 , HOH B:457BINDING SITE FOR RESIDUE GOL B 341
4AC4SOFTWAREPRO A:56 , GLN B:76 , TYR B:79 , ASP B:80 , HOH B:389 , HOH B:539 , HOH B:584BINDING SITE FOR RESIDUE GOL B 342

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3NTX)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:55 -Pro A:56
2Gln A:232 -Pro A:233
3Ala B:55 -Pro B:56
4Gln B:232 -Pro B:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NTX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NTX)

(-) Exons   (0, 0)

(no "Exon" information available for 3NTX)

(-) 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:331
 aligned with Q7CIH5_YERPE | Q7CIH5 from UniProtKB/TrEMBL  Length:338

    Alignment length:336
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331      
         Q7CIH5_YERPE     2 QKKSIYVAYTGGTIGMQRSDNGYIPVSGHLQRQLALMPEFHRPEMPDFTIHEYAPLIDSSDMTPEDWQHIANDIQQNYDLYDGFVILHGTDTMAFTASALSFMLENLAKPVIITGSQIPLAELRSDGQTNLLNALYLAANHPVNEVSLFFNNQLFRGNRTTKAHADGFDAFASPNLSVLLEAGIHIRRQSSVVSPTSNGPLIVHRITPQPIGVVTIYPGISGAVVRNFLLQPVKALILRSYGVGNAPQKAELLDELKNASDRGIVVVNLTQCISGSVNMGGYATGNALAQAGVISGFDMTVEAALTKLHYLLSQSLSPNEIRQLMQQNLRGELTDT 337
               SCOP domains d3ntxa_ A: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee..hhhhheee..eee...hhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhee.....eeee..........hhhhhhhhhhhhhhhhh....eeeee..eeee.hhheeee.....eee.......eee...eee.............ee.......eeeee.....hhhhhhhhh.....eeeeee........hhhhhhhhhhhhhh..eeeeee.........-----.hhhhhh..ee....hhhhhhhhhhhhhh...hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ntx A   2 QKKSIYVAYTGGTIGmQRSDNGYIPVSGHLQRQLALmPEFHRPEmPDFTIHEYAPLIDSSDmTPEDWQHIANDIQQNYDLYDGFVILHGTDTmAFTASALSFmLENLAKPVIITGSQIPLAELRSDGQTNLLNALYLAANHPVNEVSLFFNNQLFRGNRTTKAHADGFDTFASPNLSVLLEAGIHIRRQSSVVSPTSNGPLIVHRITPQPIGVVTIYPGISGAVVRNFLLQPVKALILRSYGVGNAPQKAELLDELKNASDRGIVVVNLTQCISGSVNm-----GNALAQAGVISGFDmTVEAALTKLHYLLSQSLSPNEIRQLmQQNLRGELTDT 337
                                    11     |  21        31      | 41    |   51        61 |      71        81        91  |    101  |    111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        |-    |  291       301       311       321    |  331      
                                          17-MSE               38-MSE  46-MSE           63-MSE                         94-MSE   104-MSE                                                                                                                                                                         280-MSE86           300-MSE                   326-MSE       


Chain B from PDB  Type:PROTEIN  Length:331
 aligned with Q7CIH5_YERPE | Q7CIH5 from UniProtKB/TrEMBL  Length:338

    Alignment length:336
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331      
         Q7CIH5_YERPE     2 QKKSIYVAYTGGTIGMQRSDNGYIPVSGHLQRQLALMPEFHRPEMPDFTIHEYAPLIDSSDMTPEDWQHIANDIQQNYDLYDGFVILHGTDTMAFTASALSFMLENLAKPVIITGSQIPLAELRSDGQTNLLNALYLAANHPVNEVSLFFNNQLFRGNRTTKAHADGFDAFASPNLSVLLEAGIHIRRQSSVVSPTSNGPLIVHRITPQPIGVVTIYPGISGAVVRNFLLQPVKALILRSYGVGNAPQKAELLDELKNASDRGIVVVNLTQCISGSVNMGGYATGNALAQAGVISGFDMTVEAALTKLHYLLSQSLSPNEIRQLMQQNLRGELTDT 337
               SCOP domains d3ntxb_ B: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---Asparaginase-3ntxB01 B:5-323                                                                                                                                                                                                                                                                                                   -------------- Pfam domains (1)
           Pfam domains (2) ---Asparaginase-3ntxB02 B:5-323                                                                                                                                                                                                                                                                                                   -------------- Pfam domains (2)
         Sec.struct. author ...eeeeee..hhhhheee..eee...hhhhhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhee.....eeee..........hhhhhhhhhhhhhhhhh....eeeee..eeee.hhheeee.....eee.......eee...eee.............ee.......eeeee.....hhhhhhhhh.....eeeeee........hhhhhhhhhhhhhh..eeeeee.........-----.hhhhhh..ee....hhhhhhhhhhhhhh...hhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ntx B   2 QKKSIYVAYTGGTIGmQRSDNGYIPVSGHLQRQLALmPEFHRPEmPDFTIHEYAPLIDSSDmTPEDWQHIANDIQQNYDLYDGFVILHGTDTmAFTASALSFmLENLAKPVIITGSQIPLAELRSDGQTNLLNALYLAANHPVNEVSLFFNNQLFRGNRTTKAHADGFDTFASPNLSVLLEAGIHIRRQSSVVSPTSNGPLIVHRITPQPIGVVTIYPGISGAVVRNFLLQPVKALILRSYGVGNAPQKAELLDELKNASDRGIVVVNLTQCISGSVNm-----GNALAQAGVISGFDmTVEAALTKLHYLLSQSLSPNEIRQLmQQNLRGELTDT 337
                                    11     |  21        31      | 41    |   51        61 |      71        81        91  |    101  |    111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271        |-    |  291       301       311       321    |  331      
                                          17-MSE               38-MSE  46-MSE           63-MSE                         94-MSE   104-MSE                                                                                                                                                                         280-MSE86           300-MSE                   326-MSE
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NTX)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Asparaginase] (13)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q7CIH5_YERPE | Q7CIH5)
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: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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