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(-) Description

Title :  THE HIGH RESOLUTION STRUCTURES OF RMLC FROM STREPTOCCUS SUIS IN COMPLEX WITH DTDP-D-GLUCOSE
 
Authors :  C. Dong, L. L. Major, A. Allen, W. Blankenfeldt, D. Maskell, J. H. Naismi
Date :  14 Feb 03  (Deposition) - 24 Jun 03  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Jelly Roll-Like Structure; Beta Sheet, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dong, L. L. Major, A. Allen, W. Blankenfeldt, D. Maskell, J. H. Naismith
High-Resolution Structures Of Rmlc From Streptococcus Suis In Complex With Substrate Analogs Locate The Active Site Of This Class Of Enzyme
Structure V. 11 715 2003
PubMed-ID: 12791259  |  Reference-DOI: 10.1016/S0969-2126(03)00098-4

(-) Compounds

Molecule 1 - DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RMLC
    Organism Scientific: STREPTOCOCCUS SUIS
    Organism Taxid: 1307
    Strain: SEROTYPE 2
    Synonym: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1DAU2Ligand/Ion2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:33 , PHE A:36 , GLU A:38 , GLN B:61 , ASN B:63 , SER B:65 , ARG B:73 , HIS B:76 , GLU B:78 , LYS B:82 , ASN B:127 , TYR B:140 , TRP B:146 , LYS B:151 , HOH B:5024 , HOH B:5095 , HOH B:5110 , HOH B:5152 , HOH B:5180 , HOH B:5237BINDING SITE FOR RESIDUE DAU B 5001
2AC2SOFTWAREGLN A:61 , ASN A:63 , SER A:65 , ARG A:73 , HIS A:76 , GLU A:78 , LYS A:82 , ASN A:127 , TYR A:140 , TRP A:146 , HOH A:9005 , HOH A:9024 , HOH A:9027 , HOH A:9032 , HOH A:9036 , HOH A:9037 , HOH A:9047 , HOH A:9156 , HIS B:29 , ARG B:33 , PHE B:36 , GLU B:38 , HOH B:5060 , HOH B:5097BINDING SITE FOR RESIDUE DAU A 9001

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:74 -Leu A:75
2Gly B:74 -Leu B:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NYW)

(-) 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:194
 aligned with Q8GIQ0_STRSU | Q8GIQ0 from UniProtKB/TrEMBL  Length:197

    Alignment length:194
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    
         Q8GIQ0_STRSU     4 NFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
               SCOP domains d1nywa_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                               SCOP domains
               CATH domains 1nywA00 A:4-197 Jelly Rolls                                                                                                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.......eeee..eeee..eeeeeeeehhhhhhhh.hhhhh.....eeeeeeee...eeeeee....eeeee.....eeeeeee.........eeeeee...eeeee...eeeeeee...eeeeeeee....hhhhhhhhee....................hhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nyw A   4 NFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193    


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with Q8GIQ0_STRSU | Q8GIQ0 from UniProtKB/TrEMBL  Length:197

    Alignment length:195
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     
         Q8GIQ0_STRSU     3 ENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
               SCOP domains d1nywb_ B: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                SCOP domains
               CATH domains 1nywB00 B:3-197 Jelly Rolls                                                                                                                                                                         CATH domains
           Pfam domains (1) -----------dTDP_sugar_isom-1nywB01 B:14-189                                                                                                                                                -------- Pfam domains (1)
           Pfam domains (2) -----------dTDP_sugar_isom-1nywB02 B:14-189                                                                                                                                                -------- Pfam domains (2)
         Sec.struct. author ........eeee.......eeee..eeee..eeeeeeeehhhhhhhh.hhhhhh....eeeeeeee...eeeeee....eeeee.....eeeeeee.........eeeeee...eeeee...eeeeeee...eeeeeeee....hhhhhhhhee....................hhhhhh..hhhhh........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nyw B   3 ENFFGKTLAARPVEAIPGMLEFDIPVHGDNRGWFKENFQKEKMLPLGFPESFFAEGKLQNNVSFSRKNVLRGLHAEPWDKYISVADGGKVLGTWVDLREGETFGNTYQTVIDASKSIFVPRGVANGFQVLSDFVAYSYLVNDYWALELKPKYAFVNYADPSLDIKWENLEEAEVSEADENHPFLKDVKPLRKEDL 197
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192
   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: 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  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8GIQ0_STRSU | Q8GIQ0)
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.

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  5.1.3.13
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 Related Entries

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

UniProtKB/TrEMBL
        Q8GIQ0_STRSU | Q8GIQ0: 1nxm 1nzc 2ixl

(-) Related Entries Specified in the PDB File

1nxm APO STRUCTURE OF RMLC FROM STREPTOCCUS SUIS
1nzc RMLC STRUCTURE FROM STREPTOCOCCUS SUIS 2 IN COMPLEX WITH THYMIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE