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(-) Description

Title :  THE STRUCTURE OF A D-LYXOSE ISOMERASE FROM THE SIGMAB REGULON OF BACILLUS SUBTILIS
 
Authors :  J. Marles-Wright, R. J. Lewis
Date :  07 Dec 10  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.23
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Isomerase, Carbohydrate Metabolism, Metal-Binding, Sugar Isomerase, Stress Response (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Marles-Wright, R. J. Lewis
The Structure Of A D-Lyxose Isomerase From The Sigmab Regulon Of Bacillus Subtilis
Proteins V. 79 2015 2011
PubMed-ID: 21520290  |  Reference-DOI: 10.1002/PROT.23028

(-) Compounds

Molecule 1 - PROBABLE D-LYXOSE KETOL-ISOMERASE
    Chains: A
    EC Number: 5.3.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS
    Organism Taxid: 224308
    Other Details: ZINC AND ARSENIC COORDINATION IN ACTIVE SITE
    Strain: 168

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1ARS1Ligand/IonARSENIC
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1ARS2Ligand/IonARSENIC
2MSE4Mod. Amino AcidSELENOMETHIONINE
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:69 , HIS A:71 , GLU A:82 , HIS A:137 , ARS A:1176 , HOH A:2262 , HOH A:2263BINDING SITE FOR RESIDUE ZN A1173
2AC2SOFTWARELYS A:90 , TYR A:92 , GLY A:142 , GLU A:143 , HOH A:2264 , HOH A:2265 , HOH A:2266BINDING SITE FOR RESIDUE SO4 A1174
3AC3SOFTWARETHR A:50 , ASP A:51 , GLN A:81 , HOH A:2116 , HOH A:2267 , HOH A:2268BINDING SITE FOR RESIDUE SO4 A1175
4AC4SOFTWAREGLU A:150 , ZN A:1173 , HOH A:2234 , HOH A:2263BINDING SITE FOR RESIDUE ARS A1176

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y0O)

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y0O)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y0O)

(-) 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    
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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:171
 aligned with DLYKI_BACSU | P96578 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:171
                                                                                                                                                                                               167     
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     |   - 
          DLYKI_BACSU     2 GITKEEVNSYYQKAGIVLTDEEVDQIQLMDYGLGKERKVGLQLFVYVNTDRYCSKELVLFPGQTCPEHRHPPVDGQEGKQETFRCRYGKVYLYVEGEKTPLPKVLPPQEDREHYTVWHEIELEPGGQYTIPPNTKHWFQAGEEGAVVTEMSSTSTDKHDIFTDPRI-----   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh....hhhhhh..eee...........eeeeeeee...eeeeeeee....eeeeee...........eeeeeeeeeeeeee............hhhhhhhh...eeeee....eeee.....eeeeeeeeeeeeeeeee..hhhhhee.....hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y0o A   2 GITKEEVNSYYQKAGIVLTDEEVDQIQLmDYGLGKERKVGLQLFVYVNTDRYCSKELVLFPGQTCPEHRHPPVDGQEGKQETFRCRYGKVYLYVEGEKTPLPKVLPPQEDREHYTVWHEIELEPGGQYTIPPNTKHWFQAGEEGAVVTEmSSTSTDKHDIFTDPRILEHHH 172
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 
                                                       30-MSE                                                                                                                  151-MSE
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2Y0O)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y0O)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (DLYKI_BACSU | P96578)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.

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