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(-) Description

Title :  CRYSTAL STRUCTURE OF A NOVEL SUGAR ISOMERASE FROM E. COLI O157:H7
 
Authors :  L. M. Van Staalduinen, Z. Jia, Montreal-Kingston Bacterial Struct Genomics Initiative (Bsgi)
Date :  10 Nov 09  (Deposition) - 21 Jul 10  (Release) - 05 Jan 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cupin Beta-Barrel, Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Van Staalduinen, C. S. Park, S. J. Yeom, M. A. Adams-Cioaba, D. K. Oh, Z. Jia
Structure-Based Annotation Of A Novel Sugar Isomerase From The Pathogenic E. Coli O157:H7.
J. Mol. Biol. V. 401 866 2010
PubMed-ID: 20615418  |  Reference-DOI: 10.1016/J.JMB.2010.06.063

(-) Compounds

Molecule 1 - D-LYXOSE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: DL41 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ECS5070, Z5688
    Organism Scientific: ESCHERICHIA COLI O157:H7
    Organism Taxid: 83334

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 14)

Asymmetric/Biological Unit (5, 14)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3IPH1Ligand/IonPHENOL
4MN2Ligand/IonMANGANESE (II) ION
5MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:104 , GLY A:168 , HOH A:429 , HOH A:442 , HOH A:464BINDING SITE FOR RESIDUE GOL A 228
2AC2SOFTWAREHIS A:23 , LEU A:24 , HOH A:337 , HOH A:428BINDING SITE FOR RESIDUE ACT A 229
3AC3SOFTWAREHIS A:103 , HIS A:105 , GLU A:110 , HIS A:171 , HOH A:251 , HOH A:339BINDING SITE FOR RESIDUE MN A 1001
4AC4SOFTWAREPHE B:58 , LYS B:90 , HIS B:103 , ASP B:193 , ASN B:197 , PHE B:199 , ARG B:205 , HOH B:255BINDING SITE FOR RESIDUE IPH B 228
5AC5SOFTWARETRP B:106 , PRO B:167 , GLY B:168 , HOH B:470BINDING SITE FOR RESIDUE GOL B 229
6AC6SOFTWAREHIS B:103 , HIS B:105 , GLU B:110 , HIS B:171 , HOH B:266 , HOH B:267BINDING SITE FOR RESIDUE MN B 1002

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:86 -B:86

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Mse A:81 -Pro A:82
2Mse B:81 -Pro B:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KMH)

(-) 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:219
 aligned with Q8X5Q7_ECO57 | Q8X5Q7 from UniProtKB/TrEMBL  Length:227

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         Q8X5Q7_ECO57     1 MKRSAINDILGHTRQFFSQHDVHLPPFASFSPAQWQQLDTAAWEEVFDLKLGWDVTAFGRNNFAAHGLTLFTLRNGSAKGMPYVKCYAEKIMHVRDAQVTPMHFHWRKREDIINRGGGNLIVELWNADSNEQTADSDITVVIDGCRQKHTAGSQLRLSPGESICLPPGLYHSFWAEAGFGDVLVGEVSSVNDDDHDNHFLQPLDRYNLIDEDEPAQLVLCNEY 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh.....hhhhhhh..eeeee...........eeeeeee............eeeeeeee....eeeeeee....eeeeeeee..eeeeeee...........eeeee..eeeee....eeee....eeee...eeeeeee......eeeeeeee.......eee....----................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kmh A   1 mKRSAINDILGHTRQFFSQHDVHLPPFASFSPAQWQQLDTAAWEEVFDLKLGWDVTAFGRNNFAAHGLTLFTLRNGSAKGmPYVKCYAEKImHVRDAQVTPmHFHWRKREDIINRGGGNLIVELWNADSNEQTADSDITVVIDGCRQKHTAGSQLRLSPGESICLPPGLYHSFWAEAGFGDVLVGEVSSVNDDDHDNHFLQPL----LIDEDEPAQLVLCNEY 223
                            |       10        20        30        40        50        60        70        80|       90 |     100 |     110       120       130       140       150       160       170       180       190       200  |    210       220   
                            |                                                                              81-MSE     92-MSE   102-MSE                                                                                              203  208               
                            1-MSE                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:223
 aligned with Q8X5Q7_ECO57 | Q8X5Q7 from UniProtKB/TrEMBL  Length:227

    Alignment length:223
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220   
         Q8X5Q7_ECO57     1 MKRSAINDILGHTRQFFSQHDVHLPPFASFSPAQWQQLDTAAWEEVFDLKLGWDVTAFGRNNFAAHGLTLFTLRNGSAKGMPYVKCYAEKIMHVRDAQVTPMHFHWRKREDIINRGGGNLIVELWNADSNEQTADSDITVVIDGCRQKHTAGSQLRLSPGESICLPPGLYHSFWAEAGFGDVLVGEVSSVNDDDHDNHFLQPLDRYNLIDEDEPAQLVLCNEY 223
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) DUF1498-3kmhB01 B:1-223                                                                                                                                                                                                         Pfam domains (1)
           Pfam domains (2) DUF1498-3kmhB02 B:1-223                                                                                                                                                                                                         Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh......hhhhhhhh.eeeee...........eeeeeee............eeeeeeee....eeeeeee....eeeeeeee..eeeeeee...........eeeee..eeeee....eeee....eeee...eeeeeee......eeeeeeee.......eee........................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kmh B   1 mKRSAINDILGHTRQFFSQHDVHLPPFASFSPAQWQQLDTAAWEEVFDLKLGWDVTAFGRNNFAAHGLTLFTLRNGSAKGmPYVKCYAEKImHVRDAQVTPmHFHWRKREDIINRGGGNLIVELWNADSNEQTADSDITVVIDGCRQKHTAGSQLRLSPGESICLPPGLYHSFWAEAGFGDVLVGEVSSVNDDDHDNHFLQPLDRYNLIDEDEPAQLVLCNEY 223
                            |       10        20        30        40        50        60        70        80|       90 |     100 |     110       120       130       140       150       160       170       180       190       200       210       220   
                            1-MSE                                                                          81-MSE     92-MSE   102-MSE
   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  (0, 0)

(no "SCOP Domain" information available for 3KMH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8X5Q7_ECO57 | Q8X5Q7)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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

UniProtKB/TrEMBL
        Q8X5Q7_ECO57 | Q8X5Q7: 3mpb

(-) Related Entries Specified in the PDB File

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