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(-) Description

Title :  CRYSTAL STRUCTURE OF D-RIBOSE-5-PHOSPHATE ISOMERASE (RPIA) FROM ESCHERICHIA COLI.
 
Authors :  E. S. Rangarajan, J. Sivaraman, A. Matte, M. Cygler, Montreal- Kingston Bacterial Structural Genomics Initiative (Bsgi)
Date :  26 Apr 02  (Deposition) - 08 May 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Crystal Structure, Ribose Phosphate Isomerase, Rpia, Montreal-Kingston Bacterial Structural Genomics Initiative, Bsgi, Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. S. Rangarajan, J. Sivaraman, A. Matte, M. Cygler
Crystal Structure Of D-Ribose-5-Phosphate Isomerase (Rpia) From Escherichia Coli
Proteins V. 48 737 2002
PubMed-ID: 12211039  |  Reference-DOI: 10.1002/PROT.10203
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOSE 5-PHOSPHATE ISOMERASE A
    Chains: A, B
    EC Number: 5.3.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DL41
    Expression System Taxid: 562
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Strain: MC1061
    Synonym: RPIA, PHOSPHORIBOISOMERASE A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric/Biological Unit (1, 14)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1LKZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LKZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LKZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LKZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LKZ)

(-) Exons   (0, 0)

(no "Exon" information available for 1LKZ)

(-) 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 RPIA_ECOLI | P0A7Z0 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           RPIA_ECOLI     1 MTQDELKKAVGWAALQYVQPGTIVGVGTGSTAAHFIDALGTMKGQIEGAVSSSDASTEKLKSLGIHVFDLNEVDSLGIYVDGADEINGHMQMIKGGGAALTREKIIASVAEKFICIADASKQVDILGKFPLPVEVIPMARSAVARQLVKLGGRPEYRQGVVTDNGNVILDVHGMEILDPIAMENAINAIPGVVTVGLFANRGADVALIGTPDGVKTIVK 219
               SCOP domains d1lkza1 A:1-126,A:199-219 D-ribose-5-phosphate isomerase (RpiA), catalytic domain                                             d1lkza2 A:127-198 D-ribose-5-phosphate isomerase (RpiA), lid domain     d1lkza1               SCOP domains
               CATH domains -1lkzA01 A:2-124,A:197-219  [code=3.40.50.1360, no name defined]                                                            1lkzA02 A:125-196  [code=3.30.70.260, no name defined]                  1lkzA01                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhh......eeee.hhhhhhhhhhh...eehhhhh..eeeeee...ee.....ee.....hhhhhhhhhhheeeeeeeee.hhh........eeeee...hhhhhhhhhhhhh.eeee..........eeeeee.....hhhhhhhhhhh...eeee.ee......eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lkz A   1 mTQDELKKAVGWAALQYVQPGTIVGVGTGSTAAHFIDALGTmKGQIEGAVSSSDASTEKLKSLGIHVFDLNEVDSLGIYVDGADEINGHmQmIKGGGAALTREKIIASVAEKFICIADASKQVDILGKFPLPVEVIPmARSAVARQLVKLGGRPEYRQGVVTDNGNVILDVHGmEILDPIAmENAINAIPGVVTVGLFANRGADVALIGTPDGVKTIVK 219
                            |       10        20        30        40 |      50        60        70        80        90 |     100       110       120       130       140       150       160       170   |   180 |     190       200       210         
                            |                                       42-MSE                                          90-MSE                                         138-MSE                             174-MSE 182-MSE                                 
                            1-MSE                                                                                     92-MSE                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:219
 aligned with RPIA_ECOLI | P0A7Z0 from UniProtKB/Swiss-Prot  Length:219

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
           RPIA_ECOLI     1 MTQDELKKAVGWAALQYVQPGTIVGVGTGSTAAHFIDALGTMKGQIEGAVSSSDASTEKLKSLGIHVFDLNEVDSLGIYVDGADEINGHMQMIKGGGAALTREKIIASVAEKFICIADASKQVDILGKFPLPVEVIPMARSAVARQLVKLGGRPEYRQGVVTDNGNVILDVHGMEILDPIAMENAINAIPGVVTVGLFANRGADVALIGTPDGVKTIVK 219
               SCOP domains d1lkzb1 B:1-126,B:199-219 D-ribose-5-phosphate isomerase (RpiA), catalytic domain                                             d1lkzb2 B:127-198 D-ribose-5-phosphate isomerase (RpiA), lid domain     d1lkzb1               SCOP domains
               CATH domains -1lkzB01 B:2-124,B:197-219  [code=3.40.50.1360, no name defined]                                                            1lkzB02 B:125-196  [code=3.30.70.260, no name defined]                  1lkzB01                 CATH domains
           Pfam domains (1) ----------------------------------------------Rib_5-P_isom_A-1lkzB01 B:47-215                                                                                                                                          ---- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------Rib_5-P_isom_A-1lkzB02 B:47-215                                                                                                                                          ---- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhh......eeee.hhhhhhhhhh....eehhhhh..eeeeee...ee.....ee.....hhhhhhhhhhheeeeeeeee.hhh........eeeee...hhhhhhhhhhhh..eeee..........eeeeee.....hhhhhhhhhhh...eeee.ee......eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lkz B   1 mTQDELKKAVGWAALQYVQPGTIVGVGTGSTAAHFIDALGTmKGQIEGAVSSSDASTEKLKSLGIHVFDLNEVDSLGIYVDGADEINGHmQmIKGGGAALTREKIIASVAEKFICIADASKQVDILGKFPLPVEVIPmARSAVARQLVKLGGRPEYRQGVVTDNGNVILDVHGmEILDPIAmENAINAIPGVVTVGLFANRGADVALIGTPDGVKTIVK 219
                            |       10        20        30        40 |      50        60        70        80        90 |     100       110       120       130       140       150       160       170   |   180 |     190       200       210         
                            1-MSE                                   42-MSE                                          90-MSE                                         138-MSE                             174-MSE 182-MSE                                 
                                                                                                                      92-MSE
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: ISOCOT_Fold (53)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RPIA_ECOLI | P0A7Z0)
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:0006014    D-ribose metabolic process    The chemical reactions and pathways involving D-ribose (ribo-pentose). As beta-D-ribofuranose, D-ribose forms the glycose group of all ribonucleosides, ribonucleotides and ribonucleic acids, and also of ribose phosphates, various glycosides, some coenzymes and some forms of vitamin B12.
    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.
    GO:0009052    pentose-phosphate shunt, non-oxidative branch    The branch of the pentose-phosphate shunt which does not involve oxidation reactions. It comprises a series of sugar phosphate interconversions, starting with ribulose 5-P and producing fructose 6-P and glyceraldehyde 3-P.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RPIA_ECOLI | P0A7Z0: 1ks2 1o8b

(-) Related Entries Specified in the PDB File

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