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(-) Description

Title :  CRYSTAL STRUCTURE OF THE M131F L135A EVAD DOUBLE MUTANT
 
Authors :  A. B. Merkel, J. H. Naismith
Date :  22 Oct 04  (Deposition) - 30 Jan 07  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Epimerase, Evad, Amycolatopsis Orientalis, Double Mutant, Orf24 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Merkel, J. H. Naismith
Crystal Structure Of The M131F L135A Evad Double Mutant
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PCZA361.16
    Atcc: 31958
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Mutation: YES
    Organism Scientific: AMYCOLATOPSIS ORIENTALIS
    Organism Taxid: 31958
    Strain: COSMID PCZA361 (AJ223998)
    Synonym: DTDP-4-KETO-6-DEOXY-D-GLUCOSE-5-EPIMERASE EVAD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:3 , LYS A:5 , ALA A:34 , GLU A:37 , ALA A:38 , HOH A:2052BINDING SITE FOR RESIDUE GOL A1206
2AC2SOFTWAREPRO A:29 , THR A:49 , TYR A:76 , SER A:132 , TYR A:133 , HOH A:2041 , HOH A:2065BINDING SITE FOR RESIDUE GOL A1207
3AC3SOFTWARETYR A:64 , THR A:65 , THR A:67 , GLY A:70 , THR A:71 , LYS A:73 , GLY A:117 , VAL A:118 , HOH A:2039BINDING SITE FOR RESIDUE GOL A1208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WA4)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:61 -Ile A:62
2Thr A:67 -Pro A:68
3Pro A:68 -Pro A:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WA4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1WA4)

(-) Exons   (0, 0)

(no "Exon" information available for 1WA4)

(-) 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:205
 aligned with O52806_AMYOR | O52806 from UniProtKB/TrEMBL  Length:205

    Alignment length:205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200     
         O52806_AMYOR     1 MQARKLAVDGAIEFTPRVFADDRGLLILPYQEEAFVEAHGGPLFRVAQTIHSMSKRGVVRGIHYTVTPPGTAKYVYCARGKAMDIVIDIRVGSPTFGQWDSVLMDQQDPRAVYLPVGVGHAFVALEDDTVMSYMLSRSYVTQDELALSALDPALGLPIDIGVEPIVSDRDRVAITLAEAQRQGLLPDYTTSQEIERRLTAVPVST 205
               SCOP domains d1wa4a_ A: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains 1wa4A00 A:1-205 Jelly Rolls                                                                                                                                                                                   CATH domains
               Pfam domains --dTDP_sugar_isom-1wa4A01 A:3-179                                                                                                                                                  -------------------------- Pfam domains
         Sec.struct. author .eeee......eeee..eeee..eeee...hhhhhhhhhh.......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee........eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wa4 A   1 MQARKLAVDGAIEFTPRVFADDRGLLILPYQEEAFVEAHGGPLFRVAQTIHSMSKRGVVRGIHYTVTPPGTAKYVYCARGKAMDIVIDIRVGSPTFGQWDSVLMDQQDPRAVYLPVGVGHAFVALEDDTVFSYMASRSYVTQDELALSALDPALGLPIDIGVEPIVSDRDRVAITLAEAQRQGLLPDYTTSQEIERRLTAVPVST 205
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (O52806_AMYOR | O52806)
molecular function
    GO:0008830    dTDP-4-dehydrorhamnose 3,5-epimerase activity    Catalysis of the reaction: dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-L-mannose.

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 Related Entries

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

UniProtKB/TrEMBL
        O52806_AMYOR | O52806: 1ofn 1oi6

(-) Related Entries Specified in the PDB File

1ofn PURIFICATION, CRYSTALLISATION AND PRELIMINARY STRUCTURAL STUDIES OF DTDP-4-KETO-6-DEOXY -GLUCOSE-5-EPIMERASE (EVAD) FROM AMYCOLATOPSIS ORIENTALIS; THE FOURTH ENZYME IN THE DTDP-L-EPIVANCOSAMINE BIOSYNTHETIC PATHWAY.
1oi6 STRUCTURE DETERMINATION OF THE TMP-COMPLEX OF EVAD