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(-) Description

Title :  RMLC P AERUGINOSA NATIVE
 
Authors :  C. Dong, J. H. Naismith
Date :  08 Jul 06  (Deposition) - 11 Jul 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.54
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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
    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, DTDP-4-KETO-6-DEOXY-D-GLUCOSE 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:62 , HIS A:65 , LYS A:74 , ARG A:92 , HIS A:121 , TYR A:134 , TRP A:140 , GLU A:145 , HOH A:2029 , HOH A:2067 , HOH A:2085 , HOH A:2086 , HOH A:2087BINDING SITE FOR RESIDUE SRT A1185

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:63 -Leu A:64

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2IXJ)

(-) 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    
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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 d2ixja_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                     SCOP domains
               CATH domains 2ixjA00 A:1-184 Jelly Rolls                                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee......eeeee..eee..eee....hhhhhhhhhh......eeeeeeee...eeeeeee......eeeeeee.eeeeeeee..........eeeeeee.....eeee...eeeeeee...eeeeeeee........eee....................hhhhhh..hhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ixj A   1 SMAMKATRLAIPDVILFEPRVFGDDRGFFFESYNQRAFEEACGHPVSFVQDNHSRSARGVLRGLHYQIRQAQGKLVRATLGEVFDVAVDLRRGSPTFGQWVGERLSAENKRQMWIPAGFAHGFVVLSEYAEFLYKTTDFWAPEHERCIVWNDPELKIDWPLQDAPLLSEKDRQGKAFADADCFP 184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
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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 2IXJ)

(-) 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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 Related Entries

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

UniProtKB/Swiss-Prot
        RMLC_PSEAE | Q9HU21: 1rtv 2ixh 2ixi 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
2ixi RMLC P AUERGINOSA WITHG DTDP-XYLOSE
2ixk RMLC P AUERGINOSA WITHG DTDP-4-KETO RHAMNNOSE (THE PRODUCT OF THE REACTION)