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(-) Description

Title :  RMLC FROM SALMONELLA TYPHIMURIUM
 
Authors :  J. H. Naismith, M. F. Giraud
Date :  07 Mar 00  (Deposition) - 18 Apr 00  (Release) - 17 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase, 3, 5 Hexulose Epimerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. F. Giraud, G. A. Leonard, R. A. Field, C. Berlind, J. H. Naismith
Rmlc, The Third Enzyme Of Dtdp-L-Rhamnose Pathway, Is A New Class Of Epimerase.
Nat. Struct. Biol. V. 7 398 2000
PubMed-ID: 10802738  |  Reference-DOI: 10.1038/75178

(-) Compounds

Molecule 1 - DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Synonym: DTDP-4-KETO-6-DEOXYGLUCOSE 3,5-EPIMERASE, DTDP-L-RHAMNOSE SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ATY1Ligand/Ion3'-O-ACETYLTHYMIDINE-5'-DIPHOSPHATE
2GOL4Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
4TPE1Ligand/Ion3'-O-ACETYLTHYMIDINE-(5' DIPHOSPHATE PHENYLESTER)

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:60 , HIS A:63 , LYS A:73 , HIS A:120 , TYR A:133 , HOH A:2165BINDING SITE FOR RESIDUE SO4 A 301
2AC2SOFTWAREHIS B:63 , LYS B:73 , HIS B:120 , TYR B:133 , ATY B:1000BINDING SITE FOR RESIDUE SO4 B 302
3AC3SOFTWARELYS A:18 , GLN A:48 , ARG A:60 , TYR A:139 , SER A:167 , LYS A:169 , HOH A:2145 , HOH A:2146 , HOH A:3001 , HOH A:3002 , PHE B:20 , ARG B:24 , PHE B:27 , GLU B:29 , TYR B:139 , PRO B:141BINDING SITE FOR RESIDUE TPE A1000
4AC4SOFTWAREPHE A:27 , GLU A:29 , PRO A:141 , SER A:142 , HOH A:3004 , GLN B:48 , ASN B:50 , HIS B:63 , TYR B:133 , TYR B:139 , GLU B:144 , SER B:167 , LYS B:169 , SO4 B:302 , HOH B:2050 , HOH B:2117 , HOH B:3005 , HOH B:3006 , HOH B:3007BINDING SITE FOR RESIDUE ATY B1000
5AC5SOFTWARETRP B:99 , GLY B:101 , HOH B:2147BINDING SITE FOR RESIDUE GOL B 201
6AC6SOFTWAREPHE A:20 , GLY A:25 , SER A:142BINDING SITE FOR RESIDUE GOL B 202
7AC7SOFTWARETRP A:99 , VAL A:100 , GLY A:101BINDING SITE FOR RESIDUE GOL A 203
8AC8SOFTWAREGLU A:81 , LEU A:125BINDING SITE FOR RESIDUE GOL A 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DZT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1DZT)

(-) 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:183
 aligned with RMLC_SALTY | P26394 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
           RMLC_SALTY     1 MMIVIKTAIPDVLILEPKVFGDERGFFFESYNQQTFEELIGRKVTFVQDNHSKSKKNVLRGLHFQRGENAQGKLVRCAVGEVFDVAVDIRKESPTFGQWVGVNLSAENKRQLWIPEGFAHGFVTLSEYAEFLYKATNYYSPSSEGSILWNDEAIGIEWPFSQLPELSAKDAAAPLLDQALLTE 183
               SCOP domains d1dzta_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                    SCOP domains
               CATH domains 1dztA00 A:1-183 Jelly Rolls                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......eeee...eee..eee.....hhhhhhhhh......eeeeeeee...eeeeeee.hhhh..eeeeeee.eeeeeeee..........eeeeeee....eeeee...eeeeeee...eeeeeeee........eee....................hhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dzt A   1 MMIVIKTAIPDVLILEPKVFGDERGFFFESYNQQTFEELIGRKVTFVQDNHSKSKKNVLRGLHFQRGENAQGKLVRCAVGEVFDVAVDIRKESPTFGQWVGVNLSAENKRQLWIPEGFAHGFVTLSEYAEFLYKATNYYSPSSEGSILWNDEAIGIEWPFSQLPELSAKDAAAPLLDQALLTE 183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   


Chain B from PDB  Type:PROTEIN  Length:183
 aligned with RMLC_SALTY | P26394 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180   
           RMLC_SALTY     1 MMIVIKTAIPDVLILEPKVFGDERGFFFESYNQQTFEELIGRKVTFVQDNHSKSKKNVLRGLHFQRGENAQGKLVRCAVGEVFDVAVDIRKESPTFGQWVGVNLSAENKRQLWIPEGFAHGFVTLSEYAEFLYKATNYYSPSSEGSILWNDEAIGIEWPFSQLPELSAKDAAAPLLDQALLTE 183
               SCOP domains d1dztb_ B: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                    SCOP domains
               CATH domains 1dztB00 B:1-183 Jelly Rolls                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......eeeee...............hhhhhhhhh......eeeeeeee......eeee.hhhh..eeeeeee.eeeeeeee..........eeeeeee....eeeee...eeeeeee...eeeeeeee....hhh.eeee...................hhhhhh..hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1dzt B   1 MMIVIKTAIPDVLILEPKVFGDERGFFFESYNQQTFEELIGRKVTFVQDNHSKSKKNVLRGLHFQRGENAQGKLVRCAVGEVFDVAVDIRKESPTFGQWVGVNLSAENKRQLWIPEGFAHGFVTLSEYAEFLYKATNYYSPSSEGSILWNDEAIGIEWPFSQLPELSAKDAAAPLLDQALLTE 183
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
   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  (0, 0)

(no "Pfam Domain" information available for 1DZT)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RMLC_SALTY | P26394)
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:0009243    O antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
    GO:0019305    dTDP-rhamnose biosynthetic process    The chemical reactions and pathways resulting in the formation of dTDP-rhamnose, a substance composed of rhamnose in glycosidic linkage with deoxyribosylthymine diphosphate.
    GO:0045226    extracellular polysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of polysaccharides used in extracellular structures.
    GO:0009103    lipopolysaccharide biosynthetic process    The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

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  1dzt
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 Related Entries

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

UniProtKB/Swiss-Prot
        RMLC_SALTY | P26394: 1dzr

(-) Related Entries Specified in the PDB File

1dzr RMLC FROM SALMONELLA TYPHIMURIUM