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(-) Description

Title :  STRUCTURE OF WILD-TYPE DTDP-4-KETO-6-DEOXY-D-GLUCOSE-3,4-KETOISOMERASE FROM ANEURINIBACILLUS THERMOAEROPHILUS IN COMPLEX WITH TDP
 
Authors :  M. L. Davis, J. B. Thoden, H. M. Holden
Date :  27 Mar 07  (Deposition) - 24 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Deoxysugar Biosynthesis, S-Layer Biosynthesis, Ketoisomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. L. Davis, J. B. Thoden, H. M. Holden
The X-Ray Structure Of Dtdp-4-Keto-6-Deoxy-D-Glucose-3, 4-Ketoisomerase.
J. Biol. Chem. V. 282 19227 2007
PubMed-ID: 17459872  |  Reference-DOI: 10.1074/JBC.M702529200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DTDP-6-DEOXY-3,4-KETO-HEXULOSE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FDTA
    Organism Scientific: ANEURINIBACILLUS THERMOAEROPHILUS
    Organism Taxid: 143495
    Strain: L420-91T

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL
3TYD2Ligand/IonTHYMIDINE-5'-DIPHOSPHATE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:322 , ASP B:70 , LYS B:127BINDING SITE FOR RESIDUE CL A 140
02AC2SOFTWAREARG A:33 , TYR A:114 , ARG A:121 , EDO A:147 , HOH A:162 , HOH A:195 , HOH A:197 , HOH A:289 , ILE B:11 , ARG B:15 , ALA B:20 , GLN B:122 , EDO B:141 , EDO B:142BINDING SITE FOR RESIDUE TYD A 141
03AC3SOFTWAREARG A:15 , LEU A:18 , ALA A:20 , EDO A:142 , EDO A:143 , HOH A:352 , ARG B:33 , ARG B:46 , TYR B:114 , TYR B:119 , ARG B:121 , HOH B:150 , HOH B:189 , HOH B:190 , HOH B:239 , HOH B:246 , HOH B:296 , HOH B:304BINDING SITE FOR RESIDUE TYD B 140
04AC4SOFTWAREARG A:46 , TYD A:141 , ILE B:11 , ASP B:13 , ARG B:15 , GLY B:16BINDING SITE FOR RESIDUE EDO B 141
05AC5SOFTWAREILE A:11 , ASP A:13 , ARG A:15 , GLY A:16 , SER A:17 , LEU A:18 , ARG B:46 , TYD B:140BINDING SITE FOR RESIDUE EDO A 142
06AC6SOFTWARELYS A:9 , VAL A:19 , ALA A:20 , HOH A:246 , TYD B:140BINDING SITE FOR RESIDUE EDO A 143
07AC7SOFTWAREGLU A:23 , ILE A:31 , HOH A:158 , HOH A:159 , HOH A:254 , GLU B:23 , ILE B:31BINDING SITE FOR RESIDUE EDO A 144
08AC8SOFTWAREGLU A:43 , GLU A:44 , PRO A:45 , HIS A:98 , ASP A:99 , PHE A:100 , HOH A:169 , HOH A:187BINDING SITE FOR RESIDUE EDO A 145
09AC9SOFTWARETYD A:141 , LYS B:9 , VAL B:19 , ALA B:20 , HOH B:250 , HOH B:288BINDING SITE FOR RESIDUE EDO B 142
10BC1SOFTWAREGLU B:43 , GLU B:44 , PRO B:45 , HIS B:98 , ASP B:99 , PHE B:100 , HOH B:148 , HOH B:165BINDING SITE FOR RESIDUE EDO B 143
11BC2SOFTWARELYS B:25 , ASN B:26 , ILE B:27 , PRO B:28BINDING SITE FOR RESIDUE EDO B 144
12BC3SOFTWAREGLU A:43 , GLU A:44 , LYS B:52 , LYS B:132BINDING SITE FOR RESIDUE EDO A 146
13BC4SOFTWAREARG A:46 , HIS A:49 , MET A:97 , TYD A:141 , HOH A:222 , HOH A:289BINDING SITE FOR RESIDUE EDO A 147

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2PA7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PA7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2PA7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2PA7)

(-) Exons   (0, 0)

(no "Exon" information available for 2PA7)

(-) 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:135
 aligned with FDTA_ANETH | Q6T1W8 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     
           FDTA_ANETH     2 ENKVINFKKIIDSRGSLVAIEENKNIPFSIKRVYYIFDTKGEEPRGFHAHKKLEQVLVCLNGSCRVILDDGNIIQEITLDSPAVGLYVGPAVWHEMHDFSSDCVMMVLASDYYDETDYIRQYDNFKKYIAKINLE 136
               SCOP domains d2pa7a1 A:2-136 dTDP-6-deoxy-3,4-keto-hexulose isomerase FdtA                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeee..eeeeeee..........eeeeee.......eeeeee....eeeeeee..eeeeee....eeeeee....eeeee....eeeee......eeeeee....hhh.ee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pa7 A   2 ENKVINFKKIIDSRGSLVAIEENKNIPFSIKRVYYIFDTKGEEPRGFHAHKKLEQVLVCLNGSCRVILDDGNIIQEITLDSPAVGLYVGPAVWHEMHDFSSDCVMMVLASDYYDETDYIRQYDNFKKYIAKINLE 136
                                    11        21        31        41        51        61        71        81        91       101       111       121       131     


Chain B from PDB  Type:PROTEIN  Length:134
 aligned with FDTA_ANETH | Q6T1W8 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           FDTA_ANETH     2 ENKVINFKKIIDSRGSLVAIEENKNIPFSIKRVYYIFDTKGEEPRGFHAHKKLEQVLVCLNGSCRVILDDGNIIQEITLDSPAVGLYVGPAVWHEMHDFSSDCVMMVLASDYYDETDYIRQYDNFKKYIAKINL 135
               SCOP domains d2pa7b_ B: dTDP-6-deoxy-3,4-keto-hexulose isomerase FdtA                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeee..eeeeeee..........eeeeee.......eeeeee....eeeeeee..eeeeee....eeeeee....eeeee....eeeee......eeeeee....hhh.ee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pa7 B   2 ENKVINFKKIIDSRGSLVAIEENKNIPFSIKRVYYIFDTKGEEPRGFHAHKKLEQVLVCLNGSCRVILDDGNIIQEITLDSPAVGLYVGPAVWHEMHDFSSDCVMMVLASDYYDETDYIRQYDNFKKYIAKINL 135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131
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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 2PA7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2PA7)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (FDTA_ANETH | Q6T1W8)
molecular function
    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.

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        FDTA_ANETH | Q6T1W8: 2pae 2pak 2pam

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2pae 2pak 2pam