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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE MUTAROTASE (YEAD) FROM SALMONELLA TYPHIMURIUM IN ORTHORHOMBIC FORM
 
Authors :  S. Chittori, D. K. Simanshu, H. S. Savithri, M. R. N. Murthy
Date :  25 Jul 06  (Deposition) - 23 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Salmonella Typhimurium, Carbohydrate, Aldose 1-Epimerase, Mutarotase, Yead, Galm, Sugar Phosphate, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chittori, D. K. Simanshu, H. S. Savithri, M. R. Murthy
Structure Of The Putative Mutarotase Yead From Salmonella Typhimurium: Structural Comparison With Galactose Mutarotases.
Acta Crystallogr. , Sect. D V. 63 197 2007
PubMed-ID: 17242513  |  Reference-DOI: 10.1107/S090744490604618X

(-) Compounds

Molecule 1 - PUTATIVE ENZYME RELATED TO ALDOSE 1-EPIMERASE
    Chains: A, B
    EC Number: 5.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET-C
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YEAD
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 602
    Strain: IFO12529

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:64 , PRO A:256 , ASP A:257 , HOH A:537 , HOH A:585BINDING SITE FOR RESIDUE SO4 A 300
2AC2SOFTWAREASN B:64 , PRO B:256 , ASP B:257 , HOH B:387BINDING SITE FOR RESIDUE SO4 B 301
3AC3SOFTWARESER A:124 , GLU A:125 , ARG A:128BINDING SITE FOR RESIDUE GOL A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Trp A:81 -Pro A:82
2Thr A:278 -Glu A:279
3Glu A:279 -Glu A:280
4Trp B:81 -Pro B:82
5Ser B:123 -Ser B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HTA)

(-) 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:297
 aligned with YEAD_SALTY | Q8ZPV9 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:297
                               1                                                                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
           YEAD_SALTY     - ---MINKIFALPVIEQLTPVLSRRQLDDLDLIVVDHPQVKASFALQGAHLLSWKPVGEEEVLWLSNNTPFKTGVALRGGVPICWPWFGPAAQQGLPSHGFARNLPWALKAHNEDDNGVMLTFELQSSEATRKYWPHDFTLLARFKVGKTCEIELEAHGEFATTSALHSYFNVGDIANVKVSGLGDRFIDKVNDAKEGVLTDGIQTFPDRTDRVYLNPEACSVIHDATLNRTIDVVHHHHLNVVGWNPGPALSVSMGDMPDDGYKTFVCVETVYATAPQQATEEKPSRLAQTICVAKR 294
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...ee....eeeeee..eeeeeeee..eeeeee.hhheeeeeee..........................ee................hhhhh..eeeeeee....eeeeeeee.hhhhhhhh....eeeeeeee...eeeeeeee..eeeeeee..eee..hhhh.eee....eeee.....eeee.....ee....eeeee.....eeeeee....eeeeeeee...eeeeeehhhhhhhhh.....hhhh.eeeeeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hta A  -2 ASHMINKIFALPVIEQLTPVLSRRQLDDLDLIVVDHPQVKASFALQGAHLLSWKPVGEEEVLWLSNNTPFKTGVALRGGVPICWPWFGPAAQQGLPSHGFARNLPWALKAHNEDDNGVMLTFELQSSEATRKYWPHDFTLLARFKVGKTCEIELEAHGEFATTSALHSYFNVGDIANVKVSGLGDRFIDKVNDAKEGVLTDGIQTFPDRTDRVYLNPEACSVIHDATLNRTIDVVHHHHLNVVGWNPGPALSVSMGDMPDDGYKTFVCVETVYATAPQQATEEKPSRLAQTICVAKR 294
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       


Chain B from PDB  Type:PROTEIN  Length:297
 aligned with YEAD_SALTY | Q8ZPV9 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:297
                               1                                                                                                                                                                                                                                                                                                     
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       
           YEAD_SALTY     - ---MINKIFALPVIEQLTPVLSRRQLDDLDLIVVDHPQVKASFALQGAHLLSWKPVGEEEVLWLSNNTPFKTGVALRGGVPICWPWFGPAAQQGLPSHGFARNLPWALKAHNEDDNGVMLTFELQSSEATRKYWPHDFTLLARFKVGKTCEIELEAHGEFATTSALHSYFNVGDIANVKVSGLGDRFIDKVNDAKEGVLTDGIQTFPDRTDRVYLNPEACSVIHDATLNRTIDVVHHHHLNVVGWNPGPALSVSMGDMPDDGYKTFVCVETVYATAPQQATEEKPSRLAQTICVAKR 294
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...ee....eeeeee..eeeeeeee..eeeeee.hhheeeeeee..........................ee................hhhhh..eeeeeee....eeeeeeee.hhhhhh......eeeeeeee...eeeeeeee..eeeeeee..eee..hhh.eeee....eeee.....eeee.....ee....eeeee.....eeeeee....eeeeeeee...eeeeeehhhhhhhhh.....hhhh.eeeeeeeeeeeeeee.....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hta B  -2 ASHMINKIFALPVIEQLTPVLSRRQLDDLDLIVVDHPQVKASFALQGAHLLSWKPVGEEEVLWLSNNTPFKTGVALRGGVPICWPWFGPAAQQGLPSHGFARNLPWALKAHNEDDNGVMLTFELQSSEATRKYWPHDFTLLARFKVGKTCEIELEAHGEFATTSALHSYFNVGDIANVKVSGLGDRFIDKVNDAKEGVLTDGIQTFPDRTDRVYLNPEACSVIHDATLNRTIDVVHHHHLNVVGWNPGPALSVSMGDMPDDGYKTFVCVETVYATAPQQATEEKPSRLAQTICVAKR 294
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HTA)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (YEAD_SALTY | Q8ZPV9)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0047938    glucose-6-phosphate 1-epimerase activity    Catalysis of the reaction: alpha-D-glucose 6-phosphate = beta-D-glucose 6-phosphate.
    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: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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  2hta
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 Related Entries

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

UniProtKB/Swiss-Prot
        YEAD_SALTY | Q8ZPV9: 2htb

(-) Related Entries Specified in the PDB File

1jov 1l7k 1lur 1snz 1z45