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(-) Description

Title :  1.63 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE (RFBC) FROM BACILLUS ANTHRACIS STR. AMES WITH TDP AND PPI BOUND
 
Authors :  A. S. Halavaty, M. Kuhn, G. Minasov, L. Shuvalova, K. Kwon, W. F. Anderso For Structural Genomics Of Infectious Diseases (Csgid)
Date :  11 May 11  (Deposition) - 25 May 11  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dtdp-4-Dehydrorhamnose 3, 5-Epimerase, Rhamnose Pathway, Structural Genomics, Infectious Diseases, Center For Structural Genomics Of Infectious Diseases (Csgid), Jelly Roll-Like Topology, The Enzyme Epimerizes At Two Carbon Centers, The 3 And 5 Positions Of The Sugar Ring, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Halavaty, M. Kuhn, G. Minasov, L. Shuvalova, K. Kwon, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 63 Angstrom Resolution Crystal Structure Of Dtdp-4-Dehydrorhamnose 3, 5-Epimerase (Rfbc) From Bacillus Anthracis Str. Ames With Tdp And Ppi Bound
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21/MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BAS1136, BA_1229, GBAA_1229, RFBC
    Organism Common: ANTHRAX,ANTHRAX BACTERIUM
    Organism Scientific: BACILLUS ANTHRACIS STR. AMES
    Organism Taxid: 198094
    Strain: BACILLUS ANTHRACIS STR. AMES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1POP1Ligand/IonPYROPHOSPHATE 2-
2TYD1Ligand/IonTHYMIDINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:143 , SER A:165 , LYS A:167 , ASP A:168 , HOH A:219 , HOH A:220 , HOH A:255 , HOH A:314BINDING SITE FOR RESIDUE POP A 182
2AC2SOFTWAREPHE A:26 , GLU A:28 , HOH A:258 , HOH A:307 , HOH A:313 , GLN B:46 , ASN B:48 , TYR B:138 , SER B:165 , LYS B:167 , ASP B:168 , HOH B:225 , HOH B:290BINDING SITE FOR RESIDUE TYD A 183

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RYK)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:60 -Leu A:61
2Asn A:66 -Pro A:67
3Gly B:60 -Leu B:61
4Asn B:66 -Pro B:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RYK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RYK)

(-) Exons   (0, 0)

(no "Exon" information available for 3RYK)

(-) 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:175
 aligned with Q81TP1_BACAN | Q81TP1 from UniProtKB/TrEMBL  Length:181

    Alignment length:175
                             1                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169     
         Q81TP1_BACAN     - -MKVIETNFTDAKLLEPRLFGDDRGFFTESYNKKVLETLGVTHSFVQDNVSYSAEAGTIRGLHFQKNPKAQTKLIQVMQGAIYDVIVDLRKDSPTFKQWRGYILSADNHRQLLVPKGFAHGFCTLVPHTIVMYKVDEYYSADHDSGVLWNDKELAIPWPVTSPILSDKDRILPLL 174
               SCOP domains d3ryka_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeee..eeee..eeeeeeeehhhhhhh.......eeeeeee.....eeeeeee.......eeeeeee.eeeeeeee..........eeeeeee.....eeee...eeeeeee....eeeeeee........eee...................hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ryk A   0 AMKVIETNFTDAKLLEPRLFGDDRGFFTESYNKKVLETLGVTHSFVQDNVSYSAEAGTIRGLHFQKNPKAQTKLIQVMQGAIYDVIVDLRKDSPTFKQWRGYILSADNHRQLLVPKGFAHGFCTLVPHTIVMYKVDEYYSADHDSGVLWNDKELAIPWPVTSPILSDKDRILPLL 174
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169     


Chain B from PDB  Type:PROTEIN  Length:175
 aligned with Q81TP1_BACAN | Q81TP1 from UniProtKB/TrEMBL  Length:181

    Alignment length:175
                             1                                                                                                                                                                             
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169     
         Q81TP1_BACAN     - -MKVIETNFTDAKLLEPRLFGDDRGFFTESYNKKVLETLGVTHSFVQDNVSYSAEAGTIRGLHFQKNPKAQTKLIQVMQGAIYDVIVDLRKDSPTFKQWRGYILSADNHRQLLVPKGFAHGFCTLVPHTIVMYKVDEYYSADHDSGVLWNDKELAIPWPVTSPILSDKDRILPLL 174
               SCOP domains d3rykb_ B: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---dTDP_sugar_isom-3rykB01 B:3-174                                                                                                                                              Pfam domains (1)
           Pfam domains (2) ---dTDP_sugar_isom-3rykB02 B:3-174                                                                                                                                              Pfam domains (2)
         Sec.struct. author ..eeeeee...eeeee..eeee..eeeeeeeehhhhhhh.......eeeeeee.....eeeeeee.......eeeeeee.eeeeeeee..........eeeeeee.....eeee...eeeeeee....eeeeeee....hhh.eee...................hhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ryk B   0 AMKVIETNFTDAKLLEPRLFGDDRGFFTESYNKKVLETLGVTHSFVQDNVSYSAEAGTIRGLHFQKNPKAQTKLIQVMQGAIYDVIVDLRKDSPTFKQWRGYILSADNHRQLLVPKGFAHGFCTLVPHTIVMYKVDEYYSADHDSGVLWNDKELAIPWPVTSPILSDKDRILPLL 174
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169
   Legend:   → Mismatch (orange background)
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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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RYK)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Cupin (179)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q81TP1_BACAN | Q81TP1)
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:0009243    O antigen biosynthetic process    The chemical reactions and pathways resulting in the formation of the O side chain of a lipopolysaccharide, which determines the antigenic specificity of the organism. It is made up of about 50 repeating units of a branched tetrasaccharide.
    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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