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(-) Description

Title :  MYCOBACTERIUM TUBERCULOSIS RMLC EPIMERASE (RV3465)
 
Authors :  C. -Y. Kim, C. Naranjo, G. S. Waldo, T. Lekin, B. W. Segelke, K. A. Kantard A. Zemla, T. Terwilliger, B. Rupp, Tb Structural Genomics Consort (Tbsgc)
Date :  05 Oct 03  (Deposition) - 07 Oct 03  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Epimerase, Rhamnose Pathway, Psi, Protein Structure Initiative, Tb Structural Genomics Consortium, Tb, Tbsgc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Kantardjieff, C. -Y. Kim, C. Naranjo, G. S. Waldo, T. Lekin, B. W. Segelke, A. Zemla, M. S. Park, T. Terwilliger, B. Rupp
Mycobacterium Tuberculosis Rmlc Epimerase (Rv3465): A Promising Drug-Target Structure In The Rhamnose Pathway
Acta Crystallogr. , Sect. D V. 60 895 2004
PubMed-ID: 15103135  |  Reference-DOI: 10.1107/S0907444904005323

(-) Compounds

Molecule 1 - DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
    Chains: A
    EC Number: 5.1.3.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: MODIFIED PET28B/HIS
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: HRV37
    Synonym: 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, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CME4Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE

(-) Sites  (0, 0)

(no "Site" information available for 1UPI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:60 -Leu A:61
2Leu A:66 -Pro A:67
3Pro A:67 -Pro A:68
4Asp A:161 -Gly A:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1UPI)

(-) Sequences/Alignments

Asymmetric 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:201
 aligned with RMLC_MYCTO | P9WH10 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           RMLC_MYCTO     1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEMRG 201
               SCOP domains d1upia_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                      SCOP domains
               CATH domains 1upiA00 A:1-201 Jelly Rolls                                                                                                                                                                               CATH domains
               Pfam domains --dTDP_sugar_isom-1upiA01 A:3-180                                                                                                                                                   --------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee..eeee..eeee...hhhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee........eee......................hhhhhh..hhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upi A   1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLcSAEYNPQREHTIcATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEMRG 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   |   140      |150       160       170       180       190       200 
                                                                                                                                                               134-CME      147-CME                                                  


Chain A from PDB  Type:PROTEIN  Length:201
 aligned with RMLC_MYCTU | P9WH11 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
           RMLC_MYCTU     1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLCSAEYNPQREHTICATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEMRG 201
               SCOP domains d1upia_ A: dTDP-4-dehydrorhamnose 3,5-epimerase RmlC                                                                                                                                                      SCOP domains
               CATH domains 1upiA00 A:1-201 Jelly Rolls                                                                                                                                                                               CATH domains
               Pfam domains --dTDP_sugar_isom-1upiA01 A:3-180                                                                                                                                                   --------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee..eeee..eeee...hhhhhhhhhh......eeeeeee....eeeeeee.......eeeeeee.eeeeeee...........eeeeeee.....eeee....eeeeee....eeeeeee........eee......................hhhhhh..hhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1upi A   1 MKARELDVPGAWEITPTIHVDSRGLFFEWLTDHGFRAFAGHSLDVRQVNCSVSSAGVLRGLHFAQLPPSQAKYVTCVSGSVFDVVVDIREGSPTFGRWDSVLLDDQDRRTIYVSEGLAHGFLALQDNSTVMYLcSAEYNPQREHTIcATDPTLAVDWPLVDGAAPSLSDRDAAAPSFEDVRASGLLPRWEQTQRFIGEMRG 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   |   140      |150       160       170       180       190       200 
                                                                                                                                                               134-CME      147-CME
   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, 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, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (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   (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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 Related Entries

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

UniProtKB/Swiss-Prot
        RMLC_MYCTO | P9WH10: 1pm7 2ixc
        RMLC_MYCTU | P9WH11: 1pm7 2ixc

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