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(-) Description

Title :  RMLC (DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE)STRUCTURE FROM MYCOBACTERIUM TUBERCULOSIS AND INHIBITOR DESIGN. THE APO STRUCTURE.
 
Authors :  C. Dong, J. H. Naismith, Tb Structural Genomics Consortium (Tbsgc
Date :  10 Jun 03  (Deposition) - 09 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rmlc, Beta Barrel, Main Beta Sheet Structure, Structural Genomics, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tbsgc, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Babaoglu, M. A. Page, V. C. Jones, M. R. Mcneil, C. Dong, J. H. Naismith, R. E. Lee
Novel Inhibitors Of An Emerging Target In Mycobacterium Tuberculosis; Substituted Thiazolidinones As Inhibitors Of Dtdp-Rhamnose Synthesis.
Bioorg. Med. Chem. Lett. V. 13 3227 2003
PubMed-ID: 12951098  |  Reference-DOI: 10.1016/S0960-894X(03)00673-5

(-) Compounds

Molecule 1 - RFBC
    Chains: A, B
    EC Number: 5.1.3.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET23B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RMLC (RFBC)
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Synonym: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE, DTDP-6-DEOXY-D-XYLO-4- HEXULOSE 3,5-EPIMERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:62 , LYS A:72 , HIS A:119BINDING SITE FOR RESIDUE ACT A 260
2AC2SOFTWAREHIS B:62 , LYS B:72 , HIS B:119BINDING SITE FOR RESIDUE ACT B 261
3AC3SOFTWAREMET A:1 , LYS A:2 , PRO A:16 , THR A:17BINDING SITE FOR RESIDUE GOL A 250
4AC4SOFTWAREMET B:1 , PRO B:16 , GLU B:28 , TRP B:29 , LEU B:30 , GLY B:34 , PHE B:35 , TYR B:73 , HOH B:265 , HOH B:309BINDING SITE FOR RESIDUE GOL B 251

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PM7)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:60 -Leu A:61
2Pro A:67 -Pro A:68
3Gly B:60 -Leu B:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PM7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PM7)

(-) Exons   (0, 0)

(no "Exon" information available for 1PM7)

(-) 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:199
 aligned with RMLC_MYCTO | P9WH10 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
           RMLC_MYCTO     1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEM 199
               SCOP domains d1pm7a_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                    SCOP domains
               CATH domains 1pm7A00 A:1-199 Jelly Rolls                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee...eee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee........eee......................hhhhhh..hhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pm7 A   1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEM 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         


Chain A from PDB  Type:PROTEIN  Length:199
 aligned with RMLC_MYCTU | P9WH11 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
           RMLC_MYCTU     1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEM 199
               SCOP domains d1pm7a_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                    SCOP domains
               CATH domains 1pm7A00 A:1-199 Jelly Rolls                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee...eee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee........eee......................hhhhhh..hhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pm7 A   1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEM 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         


Chain B from PDB  Type:PROTEIN  Length:199
 aligned with RMLC_MYCTO | P9WH10 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
           RMLC_MYCTO     1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEM 199
               SCOP domains d1pm7b_ B: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                    SCOP domains
               CATH domains 1pm7B00 B:1-199 Jelly Rolls                                                                                                                                                                             CATH domains
           Pfam domains (1) --dTDP_sugar_isom-1pm7B01 B:3-180                                                                                                                                                   ------------------- Pfam domains (1)
           Pfam domains (2) --dTDP_sugar_isom-1pm7B02 B:3-180                                                                                                                                                   ------------------- Pfam domains (2)
         Sec.struct. author .eeee.....eeeee...eee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee....hhh.eee......................hhhhhh..hhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pm7 B   1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEM 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         


Chain B from PDB  Type:PROTEIN  Length:199
 aligned with RMLC_MYCTU | P9WH11 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190         
           RMLC_MYCTU     1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEM 199
               SCOP domains d1pm7b_ B: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                    SCOP domains
               CATH domains 1pm7B00 B:1-199 Jelly Rolls                                                                                                                                                                             CATH domains
           Pfam domains (1) --dTDP_sugar_isom-1pm7B01 B:3-180                                                                                                                                                   ------------------- Pfam domains (1)
           Pfam domains (2) --dTDP_sugar_isom-1pm7B02 B:3-180                                                                                                                                                   ------------------- Pfam domains (2)
         Sec.struct. author .eeee.....eeeee...eee..eeeeeeeehhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee....hhh.eee......................hhhhhh..hhhhhhhh....hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pm7 B   1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEM 199
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   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  (5, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RMLC_MYCTU | P9WH11)
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.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0040007    growth    The increase in size or mass of an entire organism, a part of an organism or a cell.

Chain A,B   (RMLC_MYCTO | P9WH10)
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.

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  1pm7
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 Related Entries

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

UniProtKB/Swiss-Prot
        RMLC_MYCTO | P9WH10: 1upi 2ixc
        RMLC_MYCTU | P9WH11: 1upi 2ixc

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1PM7)