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(-) Description

Title :  STRUCTURAL STUDY OF CLOSTRIDIUM THERMOCELLUM RIBOSE-5-PHOSPHATE ISOMERASE B
 
Authors :  L. W. Kang, J. K. Kim, J. H. Jung, M. K. Hong
Date :  08 May 09  (Deposition) - 10 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  D-Ribose Phosphate Isomerase, Ctrpi B, Isomerization, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Jung, J. K. Kim, S. J. Yeom, Y. J. Ahn, D. K. Oh, L. W. Kang
Crystal Structure Of Clostridium Thermocellum Ribose-5-Phosphate Isomerase B Reveals Properties Critical For Fast Enzyme Kinetics.
Appl. Microbiol. Biotechnol. V. 90 517 2011
PubMed-ID: 21253719  |  Reference-DOI: 10.1007/S00253-011-3095-8

(-) Compounds

Molecule 1 - RIBOSE-5-PHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 28A(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CTHE_2597
    Organism Scientific: CLOSTRIDIUM THERMOCELLUM
    Organism Taxid: 203119

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:8 , GLY A:10 , GLY A:66 , HOH A:172 , HOH A:175 , HOH A:188 , HIS B:98BINDING SITE FOR RESIDUE GOL A 3968
2AC2SOFTWAREHIS A:98 , ASP B:8 , GLY B:10 , TYR B:42 , CYS B:65 , GLY B:66 , ARG B:109 , HOH B:158 , HOH B:162 , HOH B:179BINDING SITE FOR RESIDUE GOL B 3968

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HE8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:33 -Thr A:34
2Gly B:33 -Thr B:34

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HE8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HE8)

(-) Exons   (0, 0)

(no "Exon" information available for 3HE8)

(-) 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:148
 aligned with A3DIL8_CLOTH | A3DIL8 from UniProtKB/TrEMBL  Length:149

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
         A3DIL8_CLOTH     1 MKIGIGSDHGGYNLKREIADFLKKRGYEVIDFGTHGNESVDYPDFGLKVAEAVKSGECDRGIVICGTGLGISIAANKVPGIRAAVCTNSYMARMSREHNDANILALGERVVGLDLALDIVDTWLKAEFQGGRHATRVGKIGEIEKKYS 148
               SCOP domains d3he8a_ A: automated matches                                                                                                                         SCOP domains
               CATH domains 3he8A00 A:1-148  [code=3.40.1400.10, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3he8 A   1 MKIGIGSDHGGYNLKREIADFLKKRGYEVIDFGTHGNESVDYPDFGLKVAEAVKSGECDRGIVICGTGLGISIAANKVPGIRAAVCTNSYMARMSREHNDANILALGERVVGLDLALDIVDTWLKAEFQGGRHATRVGKIGEIEKKYS 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        


Chain B from PDB  Type:PROTEIN  Length:148
 aligned with A3DIL8_CLOTH | A3DIL8 from UniProtKB/TrEMBL  Length:149

    Alignment length:148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        
         A3DIL8_CLOTH     1 MKIGIGSDHGGYNLKREIADFLKKRGYEVIDFGTHGNESVDYPDFGLKVAEAVKSGECDRGIVICGTGLGISIAANKVPGIRAAVCTNSYMARMSREHNDANILALGERVVGLDLALDIVDTWLKAEFQGGRHATRVGKIGEIEKKYS 148
               SCOP domains d3he8b_ B: automated matches                                                                                                                         SCOP domains
               CATH domains 3he8B00 B:1-148  [code=3.40.1400.10, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3he8 B   1 MKIGIGSDHGGYNLKREIADFLKKRGYEVIDFGTHGNESVDYPDFGLKVAEAVKSGECDRGIVICGTGLGISIAANKVPGIRAAVCTNSYMARMSREHNDANILALGERVVGLDLALDIVDTWLKAEFQGGRHATRVGKIGEIEKKYS 148
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HE8)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A3DIL8_CLOTH | A3DIL8)
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:0004751    ribose-5-phosphate isomerase activity    Catalysis of the reaction: D-ribose 5-phosphate = D-ribulose 5-phosphate.
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.
    GO:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.

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 Related Entries

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

UniProtKB/TrEMBL
        A3DIL8_CLOTH | A3DIL8: 3hee 3ph3 3ph4

(-) Related Entries Specified in the PDB File

2vvr USING FOR MOLECULAR REPLACEMENT
3hee