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(-) Description

Title :  RMLC (DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE) CRYSTAL STRUCTURE FROM PSEUDOMONAS AERUGINOSA, APO STRUCTURE
 
Authors :  C. J. Dong, J. H. Naismith
Date :  10 Dec 03  (Deposition) - 02 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Rmlc, Main Beta Sheet Structure, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. J. Dong, J. H. Naismith
Rmlc (Dtdp-6-Deoxy-D-Xylo-4-Hexulose 3, 5-Epimerase) Crystal Structure From Pseudomonas Aeruginosa, Apo Structure
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
    Chains: A
    EC Number: 5.1.3.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET23A(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RMLC
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: RMLC, DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5- EPIMERASE

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1SRT1Ligand/IonS,R MESO-TARTARIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SRT2Ligand/IonS,R MESO-TARTARIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:59 , HIS A:62 , LYS A:71 , ARG A:89 , HIS A:118 , TYR A:131 , TRP A:137 , GLU A:142BINDING SITE FOR RESIDUE SRT A 182

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RTV)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  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:184
 aligned with RMLC_PSEAE | Q9HU21 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:184
                               1                                                                                                                                                                                    
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177    
           RMLC_PSEAE     - ---MKATRLAIPDVILFEPRVFGDDRGFFFESYNQRAFEEACGHPVSFVQDNHSRSARGVLRGLHYQIRQAQGKLVRATLGEVFDVAVDLRRGSPTFGQWVGERLSAENKRQMWIPAGFAHGFVVLSEYAEFLYKTTDFWAPEHERCIVWNDPELKIDWPLQDAPLLSEKDRQGKAFADADCFP 181
               SCOP domains d1rtva_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                     SCOP domains
               CATH domains 1rtvA00 A:-2-181 Jelly Rolls                                                                                                                                                             CATH domains
               Pfam domains -----dTDP_sugar_isom-1rtvA01 A:3-177                                                                                                                                                ---- Pfam domains
         Sec.struct. author ....eeee......eeee..eeee..eeee...hhhhhhhhhh......eeeeeeee...eeeeeee......eeeeeee.eeeeeeee..........eeeeeee.....eeee...eeeeeee...eeeeeeee........eee....................hhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rtv A  -2 SMAMKATRLAIPDVILFEPRVFGDDRGFFFESYNQRAFEEACGHPVSFVQDNHSRSARGVLRGLHYQIRQAQGKLVRATLGEVFDVAVDLRRGSPTFGQWVGERLSAENKRQMWIPAGFAHGFVVLSEYAEFLYKTTDFWAPEHERCIVWNDPELKIDWPLQDAPLLSEKDRQGKAFADADCFP 181
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177
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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  (1, 1)

Asymmetric Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (RMLC_PSEAE | Q9HU21)
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: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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        RMLC_PSEAE | Q9HU21: 2ixh 2ixi 2ixj 2ixk

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