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(-) Description

Title :  THE 1.6 A RESOLUTION CRYSTAL STRUCTURE OF NOVW: A 4-KETO-6-DEOXY SUGAR EPIMERASE FROM THE NOVOBIOCIN BIOSYNTHETIC GENE CLUSTER OF STREPTOMYCES SPHEROIDES
 
Authors :  P. Jakimowicz, M. Tello, C. L. Freel-Meyers, C. T. Walsh, M. J. Buttner, R. A. Field, D. M. Lawson
Date :  09 Sep 05  (Deposition) - 25 Jan 06  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Isomerase, Epimerase, Antibiotic Biosynthesis, Rmlc-Like Cupin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Jakimowicz, M. Tello, C. L. Freel-Meyers, C. T. Walsh, M. J. Buttner, R. A. Field, D. M. Lawson
The 1. 6 A Resolution Crystal Structure Of Novw: A 4-Keto-6-Deoxy Sugar Epimerase From The Novobiocin Biosynthetic Gene Cluster Of Streptomyces Spheroides
Proteins V. 63 261 2006
PubMed-ID: 16411240  |  Reference-DOI: 10.1002/PROT.20818
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NOVW
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: GOLD
    Expression System Vector: PET-15B
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES NIVEUS NCIMB 11891
    Organism Taxid: 1352941

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:19 , SER A:165 , ARG A:167 , HOH A:2038 , HOH A:2197 , HOH A:2198BINDING SITE FOR RESIDUE SO4 A1191
2AC2SOFTWARESER A:-1 , ARG A:-3 , THR A:15 , PRO A:16 , SER A:107 , ARG A:109 , HOH A:2199BINDING SITE FOR RESIDUE EDO A1192
3AC3SOFTWAREASP A:105 , ARG A:108 , HOH A:2035 , HOH A:2200BINDING SITE FOR RESIDUE EDO A1193
4AC4SOFTWAREPRO A:5 , ILE A:8 , GLU A:9 , GLY A:10 , VAL A:11 , TRP A:12 , HOH A:2025BINDING SITE FOR RESIDUE EDO A1194

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C0Z)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:60 -Ile A:61
2Val A:66 -Pro A:67
3Pro A:67 -Pro A:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C0Z)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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:199
 aligned with NOVW_STRNV | Q9L9E5 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:199
                                     1                                                                                                                                                                                             
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         
           NOVW_STRNV     - ---------MRLRPLGIEGVWEITPEQRADPRGVFLDWYHVDRFAEAIGRPLRLAQANLSVSVRGVVRGIHFVDVPPGQAKYVTCVRGAVFDVVVDLRVGSPTYGCWEGTRLDDVSRRAVYLSEGIGHGFCAISDEATLCYLSSGTYDPATEHGVHPLDPELAIDWPTGTPLLSPRDQDALLLAEARDAGLLPTYATCQ 190
               SCOP domains ---------d2c0za1 A:1-190 Novobiocin biosynthesis protein NovW                                                                                                                                           SCOP domains
               CATH domains ---------2c0zA01 A:1-190 Jelly Rolls                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee.....eeeee.eeeee..eeeee..hhhhhhhhhh......eeeeeeee...eeeeeee.......eeeeeee.eeeeeeee..........eeeeeee.....eeee...eeeeeee...eeeeeeee........eee...................hhhhhh..hhhhhhhh....hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c0z A  -8 SGLVPRGSHMRLRPLGIEGVWEITPEQRADPRGVFLDWYHVDRFAEAIGRPLRLAQANLSVSVRGVVRGIHFVDVPPGQAKYVTCVRGAVFDVVVDLRVGSPTYGCWEGTRLDDVSRRAVYLSEGIGHGFCAISDEATLCYLSSGTYDPATEHGVHPLDPELAIDWPTGTPLLSPRDQDALLLAEARDAGLLPTYATCQ 190
                                     1        11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "Pfam Domain" information available for 2C0Z)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (NOVW_STRNV | Q9L9E5)
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.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0017000    antibiotic biosynthetic process    The chemical reactions and pathways resulting in the formation of an antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0043642    novobiocin biosynthetic process    The chemical reactions and pathways resulting in the formation of novobiocin, a coumarin antibiotic produced by the bacterium Gyrasestreptomyces spheroides, that acts by inhibiting DNA gyrase.

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