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(-) Description

Title :  CRYSTAL STRUCTURE OF CHLORELLA VIRUS VAL-1 SOAKED IN 200MM D-GLUCURONIC ACID, 10% PEG-3350, AND 200MM GLYCINE-NAOH (PH 10.0)
 
Authors :  K. Ogura, M. Yamasaki, T. Hashidume, T. Yamada, B. Mikami, W. Hashimoto
Date :  08 Aug 09  (Deposition) - 20 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A
Keywords :  Alginate Lyase, Polysaccharide Lyase Family 14, Chlorella Virus, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ogura, M. Yamasaki, T. Yamada, B. Mikami, W. Hashimoto, K. Murata
Crystal Structure Of Family 14 Polysaccharide Lyase With Ph-Dependent Modes Of Action
J. Biol. Chem. V. 284 35572 2009
PubMed-ID: 19846561  |  Reference-DOI: 10.1074/JBC.M109.068056

(-) Compounds

Molecule 1 - VAL-1
    Chains: A
    EC Number: 4.2.2.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 106-349
    Gene: VAL-1
    Organism Scientific: CHLORELLA VIRUS
    Organism Taxid: 31555
    Strain: CVK-2
    Synonym: ALGINATE LYASE VAL-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BDP1Ligand/IonBETA-D-GLUCOPYRANURONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:50 , LYS A:92 , SER A:104 , GLY A:105 , TYR A:106 , ARG A:116 , TYR A:128 , TYR A:130 , PHE A:220 , GLY A:223 , HOH A:799BINDING SITE FOR RESIDUE BDP A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3IM0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:222 -Gly A:223
2Gly A:223 -Pro A:224

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3IM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3IM0)

(-) Exons   (0, 0)

(no "Exon" information available for 3IM0)

(-) 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    
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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:243
 aligned with Q9DTZ2_9PHYC | Q9DTZ2 from UniProtKB/TrEMBL  Length:349

    Alignment length:243
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346   
         Q9DTZ2_9PHYC   107 NVISTLDLNLLTKGGGSWNVDGVNMKKSAVTTFDGKRVVKAVYDKNSGTSANPGVGGFSFSAVPDGLNKNAITFAWEVFYPKGFDFARGGKHGGTFIGHGAASGYQHSKTGASNRIMWQEKGGVIDYIYPPSDLKQKIPGLDPEGHGIGFFQDDFKNALKYDVWNRIEIGTKMNTFKNGIPQLDGESYVIVNGKKEVLKRINWSRSPDLLISRFDWNTFFGGPLPSPKNQVAYFTNFQMKKYE 349
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhh.eeeee....eeeee..eeeeeeee..............eeeee........eeeeeeeee..........eeeeeeeee............eeeeeeee.hhh.eeeeee..................eee..............eeeeeeee...ee..ee...eeeeeee..eeeeeeee.........eeeeeeeeee.........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3im0 A   2 NVISTLDLNLLTKGGGSWNVDGVNMKKSAVTTFDGKRVVKAVYDKNSGTSANPGVGGFSFSAVPDGLNKNAITFAWEVFYPKGFDFARGGKHGGTFIGHGAASGYQHSKTGASNRIMWQEKGGVIDYIYPPSDLKQKIPGLDPEGHGIGFFQDDFKNALKYDVWNRIEIGTKMNTFKNGIPQLDGESYVIVNGKKEVLKRINWSRSPDLLISRFDWNTFFGGPLPSPKNQVAYFTNFQMKKYE 244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   Legend:   → Mismatch (orange background)
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  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 3IM0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3IM0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3IM0)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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 Related Entries

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

UniProtKB/TrEMBL
        Q9DTZ2_9PHYC | Q9DTZ2: 3a0n 3gne

(-) Related Entries Specified in the PDB File

3a0n D-GLUCURONIC ACID-BOUND VAL-1 AT PH 7.0
3gne LIGAND-FREE VAL-1