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(-) Description

Title :  STRUCTURE DETERMINATION OF THE TMP-COMPLEX OF EVAD
 
Authors :  A. B. Merkel, J. H. Naismith
Date :  09 Jun 03  (Deposition) - 03 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Epimerase, Vancomycin Group Antibiotic, Evad, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. B. Merkel, L. L. Major, J. C. Errey, M. D. Burkart, R. A. Field, C. T. Walsh, J. H. Naismith
The Position Of A Key Tyrosine In Dtdp-4-Keto-6- Deoxy-D-Glucose-5-Epimerase (Evad) Alters The Substrate Profile For This Rmlc-Like Enzyme
J. Biol. Chem. V. 279 32684 2004
PubMed-ID: 15159413  |  Reference-DOI: 10.1074/JBC.M404091200
(for further references see the PDB file header)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2TMP2Ligand/IonTHYMIDINE-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:48 , TYR A:139 , ARG A:169 , HOH A:2342 , HOH A:2343 , HOH A:2344 , HOH A:2345 , HOH A:2346 , ARG B:23 , LEU B:26 , LEU B:28BINDING SITE FOR RESIDUE TMP A1204
2AC2SOFTWAREARG A:23 , LEU A:26 , LEU A:28 , GLN B:48 , TYR B:139 , THR B:141 , GLN B:142 , ARG B:169 , HOH B:2317 , HOH B:2318 , HOH B:2319 , HOH B:2320 , HOH B:2321 , HOH B:2322 , HOH B:2323 , HOH B:2324BINDING SITE FOR RESIDUE TMP B1203
3AC3SOFTWARESER A:132 , MET A:134 , HOH A:2114 , HOH A:2339 , HOH A:2340 , HOH A:2341 , SER B:132 , MET B:134 , HOH B:2113BINDING SITE FOR RESIDUE GOL A1203
4AC4SOFTWAREHOH A:2001 , HOH A:2348 , HOH A:2349 , HOH A:2351BINDING SITE FOR RESIDUE GOL A1205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OI6)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Gly A:61 -Ile A:62
2Thr A:67 -Pro A:68
3Pro A:68 -Pro A:69
4Gly B:61 -Ile B:62
5Thr B:67 -Pro B:68
6Pro B:68 -Pro B:69

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1OI6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1OI6)

(-) Exons   (0, 0)

(no "Exon" information available for 1OI6)

(-) 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:202
 aligned with O52806_AMYOR | O52806 from UniProtKB/TrEMBL  Length:205

    Alignment length:202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  
         O52806_AMYOR     1 MQARKLAVDGAIEFTPRVFADDRGLLILPYQEEAFVEAHGGPLFRVAQTIHSMSKRGVVRGIHYTVTPPGTAKYVYCARGKAMDIVIDIRVGSPTFGQWDSVLMDQQDPRAVYLPVGVGHAFVALEDDTVMSYMLSRSYVTQDELALSALDPALGLPIDIGVEPIVSDRDRVAITLAEAQRQGLLPDYTTSQEIERRLTAVP 202
               SCOP domains d1oi6a_ A: dTDP-4-keto-6-deoxy-glucose-5-epimerase EvaD                                                                                                                                                    SCOP domains
               CATH domains 1oi6A00 A:1-202 Jelly Rolls                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......eeee...eee..eeee...hhhhhhhhhh.......eeeeeee....eeeeeee.......eeeeeee..eeeeee...........eeeeee......eeee....eeeeee....eeeeeee....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi6 A   1 MQARKLAVDGAIEFTPRVFADDRGLLILPYQEEAFVEAHGGPLFRVAQTIHSMSKRGVVRGIHYTVTPPGTAKYVYCARGKAMDIVIDIRVGSPTFGQWDSVLMDQQDPRAVYLPVGVGHAFVALEDDTVMSYMLSRSYVTQDELALSALDPALGLPIDIGVEPIVSDRDRVAITLAEAQRQGLLPDYTTSQEIERRLTAVP 202
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200  


Chain B from PDB  Type:PROTEIN  Length:203
 aligned with O52806_AMYOR | O52806 from UniProtKB/TrEMBL  Length:205

    Alignment length:203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   
         O52806_AMYOR     1 MQARKLAVDGAIEFTPRVFADDRGLLILPYQEEAFVEAHGGPLFRVAQTIHSMSKRGVVRGIHYTVTPPGTAKYVYCARGKAMDIVIDIRVGSPTFGQWDSVLMDQQDPRAVYLPVGVGHAFVALEDDTVMSYMLSRSYVTQDELALSALDPALGLPIDIGVEPIVSDRDRVAITLAEAQRQGLLPDYTTSQEIERRLTAVPV 203
               SCOP domains d1oi6b_ B: dTDP-4-keto-6-deoxy-glucose-5-epimerase EvaD                                                                                                                                                     SCOP domains
               CATH domains 1oi6B00 B:1-203 Jelly Rolls                                                                                                                                                                                 CATH domains
           Pfam domains (1) --dTDP_sugar_isom-1oi6B01 B:3-179                                                                                                                                                  ------------------------ Pfam domains (1)
           Pfam domains (2) --dTDP_sugar_isom-1oi6B02 B:3-179                                                                                                                                                  ------------------------ Pfam domains (2)
         Sec.struct. author .eeee......eeee...eee..eeee...hhhhhhhhhh.......eeeeeee....eeeeeee.......eeeeeee..eeeeee...........eeeeee......eeee....eeeeee....eeeeeee....hhh.eee....................hhhhhh..hhhhhhhh....hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oi6 B   1 MQARKLAVDGAIEFTPRVFADDRGLLILPYQEEAFVEAHGGPLFRVAQTIHSMSKRGVVRGIHYTVTPPGTAKYVYCARGKAMDIVIDIRVGSPTFGQWDSVLMDQQDPRAVYLPVGVGHAFVALEDDTVMSYMLSRSYVTQDELALSALDPALGLPIDIGVEPIVSDRDRVAITLAEAQRQGLLPDYTTSQEIERRLTAVPV 203
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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  1oi6
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  O52806_AMYOR | O52806
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 Related Entries

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

UniProtKB/TrEMBL
        O52806_AMYOR | O52806: 1ofn 1wa4

(-) 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.