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(-) Description

Title :  RMLC P AERUGINOSA WITH DTDP-XYLOSE
 
Authors :  C. Dong, J. H. Naismith
Date :  08 Jul 06  (Deposition) - 11 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Isomerase, Lipopolysaccharide Biosynthesis, Epimerise, Epimerase, Epimerize (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Dong, L. L. Major, V. Srikannathasan, J. C. Errey, M. F. Giraud, J. S. Lam, M. Graninger, P. Messner, M. R. Mcneil, R. A. Field, C. Whitfield, J. H. Naismith
Rmlc, A C3' And C5' Carbohydrate Epimerase, Appears To Operate Via An Intermediate With An Unusual Twist Boat Conformation.
J. Mol. Biol. V. 365 146 2007
PubMed-ID: 17046787  |  Reference-DOI: 10.1016/J.JMB.2006.09.063

(-) Compounds

Molecule 1 - DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: DTDP-4-KETO-6-DEOXYGLUCOSE 3,5-EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1SRT1Ligand/IonS,R MESO-TARTARIC ACID
2TYD2Ligand/IonTHYMIDINE-5'-DIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:47 , TRP A:137 , LYS A:167 , HOH A:2223 , HOH A:2224 , HOH A:2225 , HOH A:2226 , HOH A:2227 , HOH A:2228 , HOH A:2229 , PHE B:19 , ARG B:23 , PHE B:26 , GLU B:28BINDING SITE FOR RESIDUE TYD A1182
2AC2SOFTWAREHIS A:62 , LYS A:71 , HIS A:118 , TYR A:131 , HOH A:2126BINDING SITE FOR RESIDUE SRT A1183
3AC3SOFTWAREPHE A:19 , ARG A:23 , PHE A:26 , GLU A:28 , HOH A:2063 , GLN B:47 , TRP B:137 , LYS B:167 , HOH B:2183 , HOH B:2200 , HOH B:2219 , HOH B:2220 , HOH B:2222 , HOH B:2223 , HOH B:2225BINDING SITE FOR RESIDUE TYD B1182

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:60 -Leu A:61
2Gly B:60 -Leu B:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2IXI)

(-) Exons   (0, 0)

(no "Exon" information available for 2IXI)

(-) 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: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 d2ixia_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                     SCOP domains
               CATH domains 2ixiA00 A:-2-181 Jelly Rolls                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......eeee...eee..eeeeeeeehhhhhhhhh......eeeeeeee...eeeeeee......eeeeeee.eeeeeeee..........eeeeeee.....eeee...eeeeeee...eeeeeeee....hhh.eee....................hhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ixi A  -2 SMSMKATRLAIPDVILFEPRVFGDDRGFFFESYNQRAFEEACGHPVSFVQDNHSRSARGVLRGLHYQIRQAQGKLVRATLGEVFDVAVDLRRGSPTFGQWVGERLSAENKRQMWIPAGFAHGFVVLSEYAEFLYKTTDFWAPEHERCIVWNDPELKIDWPLQDAPLLSEKDRQGKAFADADCFP 181
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177    


Chain B 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 d2ixib_ B: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                     SCOP domains
               CATH domains 2ixiB00 B:-2-181 Jelly Rolls                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee......eeee...ee...eeeeeeeehhhhhhhhh......eeeeeeee...eeeeeee......eeeeeee.eeeeeeee..........eeeeeee.....eeee...eeeeeee...eeeeeeee....hhh.eee....................hhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ixi B  -2 SMSMKATRLAIPDVILFEPRVFGDDRGFFFESYNQRAFEEACGHPVSFVQDNHSRSARGVLRGLHYQIRQAQGKLVRATLGEVFDVAVDLRRGSPTFGQWVGERLSAENKRQMWIPAGFAHGFVVLSEYAEFLYKTTDFWAPEHERCIVWNDPELKIDWPLQDAPLLSEKDRQGKAFADADCFP 181
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        RMLC_PSEAE | Q9HU21: 1rtv 2ixh 2ixj 2ixk

(-) Related Entries Specified in the PDB File

1rtv RMLC (DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3, 5-EPIMERASE) CRYSTALSTRUCTURE FROM PSEUDOMONAS AERUGINOSA, APO STRUCTURE
2ixh RMLC P AUERGINOSA WITHG DTDP-RHAMNOSE
2ixj RMLC P AUERGINOSA NATIVE
2ixk RMLC P AUERGINOSA WITHG DTDP-4-KETO RHAMNNOSE (THE PRODUCT OF THE REACTION)