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(-) Description

Title :  CRYSTAL STRUCTURE OF PH0066 FROM PYROCOCCUS HORIKOSHII
 
Authors :  Ihsanawati, S. Sekine, K. Murayama, M. Sugawara, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  02 Aug 04  (Deposition) - 02 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha And Beta Proteins, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Ihsanawati, S. Sekine, K. Murayama, M. Sugawara, M. Shirouzu, S. Yokoyama
Crystal Structure Of Ph0066 From Pyrococcus Horikoshii
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-ASPARAGINASE
    Chains: A, B
    EC Number: 3.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET16A
    Expression System Strain: BL21 (DE3) CODON+
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PH0066
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , THR A:11 , SER A:52 , GLY A:82 , THR A:83 , ASP A:84 , EDO A:1002 , HOH A:1044BINDING SITE FOR RESIDUE EDO A 1001
2AC2SOFTWAREASP A:51 , SER A:52 , THR A:53 , ILE A:55 , GLY A:82 , ASP A:84 , THR A:85 , EDO A:1001BINDING SITE FOR RESIDUE EDO A 1002
3AC3SOFTWAREPRO B:169BINDING SITE FOR RESIDUE EDO B 1003
4AC4SOFTWARESER B:94 , ILE B:138 , LEU B:148 , GLY B:149 , VAL B:150 , TYR B:188 , THR B:321BINDING SITE FOR RESIDUE EDO B 1004
5AC5SOFTWAREILE B:181 , LEU B:182 , HOH B:1384BINDING SITE FOR RESIDUE EDO B 1005

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WNF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WNF)

(-) Exons   (0, 0)

(no "Exon" information available for 1WNF)

(-) 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 O57797_PYRHO | O57797 from UniProtKB/TrEMBL  Length:328

    Alignment length:326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      
         O57797_PYRHO     1 MRILILGMGGTIASVKGERGYESALSVSKILKLAGISSEAKIEARDLMNVDSTLIQPSDWERLAKEIEKEVWEYDGIVITHGTDTMAYSASMLSFMLRNPPIPIVLTGSMLPITEKNSDAPFNLRTALEFVKLGIRGIYIAFNGKVMLGVRASKIRSMGFDAFESINYPNVAEIKDDKLRILHIPDFYGDEFFSDIKYEPKVLVIKLIPGLSGDIVREALRLGYKGIILEGYGVGGIPYRGTDLFEVVSSISKRIPVVLTTQAIYDGVDLQRYKVGRIALEAGVIPAGDMTKEATITKLMWILGHTKNIEEVKQLMGKNITGELTR 326
               SCOP domains d1wnfa_ A: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhh...........hhhhhhhh....--.eeeeeeeeee.....hhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhee....eeeee...........hhhhhhhhhhhhhh....eeeeee..eeee...eee........eee......eee....eee...........ee.......eeeee......hhhhhhhhhh...eeeeee...........hhhhhhhhhh....eeeee...........hhhhhhhhhh..ee....hhhhhhhhhhhhhh...hhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wnf A   1 MRILILGMGGTIASVKGERGYESALSVSKILKLAGIS--AKIEARDLMNVDSTLIQPSDWERLAKEIEKEVWEYDGIVITHGTDTMAYSASMLSFMLRNPPIPIVLTGSMLPITEKNSDAPFNLRTALEFVKLGIRGIYIAFNGKVMLGVRASKIRSMGFDAFESINYPNVAEIKDDKLRILHIPDFYGDEFFSDIKYEPKVLVIKLIPGLSGDIVREALRLGYKGIILEGYGVGGIPYRGTDLFEVVSSISKRIPVVLTTQAIYDGVDLQRYKVGRIALEAGVIPAGDMTKEATITKLMWILGHTKNIEEVKQLMGKNITGELTR 326
                                    10        20        30      | 40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      
                                                               37 40                                                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:324
 aligned with O57797_PYRHO | O57797 from UniProtKB/TrEMBL  Length:328

    Alignment length:326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      
         O57797_PYRHO     1 MRILILGMGGTIASVKGERGYESALSVSKILKLAGISSEAKIEARDLMNVDSTLIQPSDWERLAKEIEKEVWEYDGIVITHGTDTMAYSASMLSFMLRNPPIPIVLTGSMLPITEKNSDAPFNLRTALEFVKLGIRGIYIAFNGKVMLGVRASKIRSMGFDAFESINYPNVAEIKDDKLRILHIPDFYGDEFFSDIKYEPKVLVIKLIPGLSGDIVREALRLGYKGIILEGYGVGGIPYRGTDLFEVVSSISKRIPVVLTTQAIYDGVDLQRYKVGRIALEAGVIPAGDMTKEATITKLMWILGHTKNIEEVKQLMGKNITGELTR 326
               SCOP domains d1wnfb_ B: automated matches                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Asparaginase-1wnfB01 B:2-313                                                                                                                                                                                                                                                                                            ------------- Pfam domains (1)
           Pfam domains (2) -Asparaginase-1wnfB02 B:2-313                                                                                                                                                                                                                                                                                            ------------- Pfam domains (2)
         Sec.struct. author .eeeeeeee....eee....eee..hhhhhhhhhh..--.eeeeeeeeee.....hhhhhhhhhhhhhh......eeeee....hhhhhhhhhhhhee....eeeee...........hhhhhhhhhhhhhh....eeeeee..eeee...eee........eee......eee....eee...........ee.......eeeee......hhhhhhhhhhh..eeeeee...........hhhhhhhhhh....eeeee...........hhhhhhhhhhh.ee....hhhhhhhhhhhhhh...hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wnf B   1 MRILILGMGGTIASVKGERGYESALSVSKILKLAGIS--AKIEARDLMNVDSTLIQPSDWERLAKEIEKEVWEYDGIVITHGTDTMAYSASMLSFMLRNPPIPIVLTGSMLPITEKNSDAPFNLRTALEFVKLGIRGIYIAFNGKVMLGVRASKIRSMGFDAFESINYPNVAEIKDDKLRILHIPDFYGDEFFSDIKYEPKVLVIKLIPGLSGDIVREALRLGYKGIILEGYGVGGIPYRGTDLFEVVSSISKRIPVVLTTQAIYDGVDLQRYKVGRIALEAGVIPAGDMTKEATITKLMWILGHTKNIEEVKQLMGKNITGELTR 326
                                    10        20        30      | 40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      
                                                               37 40
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1WNF)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O57797_PYRHO | O57797)
molecular function
    GO:0004067    asparaginase activity    Catalysis of the reaction: L-asparagine + H2O = L-aspartate + NH3.
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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 Related Entries

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UniProtKB/TrEMBL
        O57797_PYRHO | O57797: 1wls

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