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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOSE-5-ISOMERASE A
 
Authors :  M. Orlikowska, R. Rostankowski, C. Nakka, J. Hattne, S. Grimshaw, D. Bo Z. Otwinowski, Center For Structural Genomics Of Infectious D (Csgid)
Date :  01 Dec 09  (Deposition) - 05 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Isomerase, Structural Genomics, Idp02119, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  

PubMed: search

(-) Compounds

Molecule 1 - RIBOSE-5-PHOSPHATE ISOMERASE A
    Chains: A, B, C, D
    EC Number: 5.3.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: ROSETTA(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: FTT1208, FTW_1255, RPIA
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. TULARENSIS
    Organism Taxid: 119856
    Strain: SCHU S4
    Synonym: PHOSPHORIBOISOMERASE A, PRI

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
13GR1Ligand/IonGLYCERALDEHYDE
2NA2Ligand/IonSODIUM ION
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
4PO43Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
13GR1Ligand/IonGLYCERALDEHYDE
2NA-1Ligand/IonSODIUM ION
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
4PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
13GR-1Ligand/IonGLYCERALDEHYDE
2NA-1Ligand/IonSODIUM ION
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
4PO41Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:198 , VAL A:199 , HOH A:241 , VAL D:198 , VAL D:199 , HOH D:234BINDING SITE FOR RESIDUE NA A 225
02AC2SOFTWARESER A:36 , THR A:37 , LYS A:127 , HOH A:240 , HOH A:260 , HOH A:261BINDING SITE FOR RESIDUE PO4 A 226
03AC3SOFTWAREVAL B:198 , VAL B:199 , VAL C:198 , VAL C:199BINDING SITE FOR RESIDUE NA B 225
04AC4SOFTWARELYS B:13 , SER B:36 , THR B:37 , LYS B:127 , HOH B:254 , HOH B:287BINDING SITE FOR RESIDUE PO4 B 226
05AC5SOFTWAREGLN C:165 , ILE C:167 , ASP C:169BINDING SITE FOR RESIDUE PEG C 225
06AC6SOFTWAREGLY C:39 , GLU C:43 , LYS C:65 , HOH C:277BINDING SITE FOR RESIDUE PEG C 226
07AC7SOFTWARETYR C:162 , HOH C:242BINDING SITE FOR RESIDUE PEG C 227
08AC8SOFTWAREASN C:134 , GLN C:159BINDING SITE FOR RESIDUE PEG C 228
09AC9SOFTWAREGLY D:35 , ALA D:89 , ASP D:90 , LYS D:100 , GLY D:101 , GLY D:102 , GLY D:103 , PO4 D:226 , HOH D:277BINDING SITE FOR RESIDUE 3GR D 225
10BC1SOFTWARELYS D:13 , SER D:36 , THR D:37 , ALA D:89 , LYS D:127 , 3GR D:225 , HOH D:289 , HOH D:300BINDING SITE FOR RESIDUE PO4 D 226

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KWM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KWM)

(-) 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:218
 aligned with RPIA_FRATT | Q5NFM5 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:218
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        
           RPIA_FRATT     7 NNQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------3kwmA02 A:131-202  [code=3.30.70.260, no name defined]                  ---------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhh.....hhhhhh.eeeeee...ee.....ee.....hhhhhhhhhhheeeeeeeee.hhh........eeeee...hhhhhhhhhhhh..eeee..........eeeeee.....hhhhhhhhhhh...eeee.ee......eeeee.....eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kwm A   7 NNQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with RPIA_FRATT | Q5NFM5 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:217
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       
           RPIA_FRATT     8 NQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------3kwmB02 B:131-202  [code=3.30.70.260, no name defined]                  ---------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh.....hhhhhh.eeeeee...ee.....ee.....hhhhhhhhhhheeeeeeeee.hhh........eeeee...hhhhhhhhhhhh..eeee..........eeeeee.....hhhhhhhhhh....eeee.ee......eeeee.....eeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kwm B   8 NQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       


Chain C from PDB  Type:PROTEIN  Length:218
 aligned with RPIA_FRATT | Q5NFM5 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:218
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        
           RPIA_FRATT     7 NNQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------3kwmC02 C:131-202  [code=3.30.70.260, no name defined]                  ---------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh.....hhhhhh.eeeeee...ee.....ee.....hhhhhhhhhhheeeeeeeee.hhh........eeeee...hhhhhhhhhhhh..eeee..........eeeeee.....hhhhhhhhhhh...eeee.ee......eeeeee...eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kwm C   7 NNQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        


Chain D from PDB  Type:PROTEIN  Length:218
 aligned with RPIA_FRATT | Q5NFM5 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:218
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216        
           RPIA_FRATT     7 NNQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------3kwmD02 D:131-202  [code=3.30.70.260, no name defined]                  ---------------------- CATH domains
           Pfam domains (1) ----------------------------------------------Rib_5-P_isom_A-3kwmD01 D:53-221                                                                                                                                          --- Pfam domains (1)
           Pfam domains (2) ----------------------------------------------Rib_5-P_isom_A-3kwmD02 D:53-221                                                                                                                                          --- Pfam domains (2)
           Pfam domains (3) ----------------------------------------------Rib_5-P_isom_A-3kwmD03 D:53-221                                                                                                                                          --- Pfam domains (3)
           Pfam domains (4) ----------------------------------------------Rib_5-P_isom_A-3kwmD04 D:53-221                                                                                                                                          --- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhhhh.....hhhhhh.eeeeee...ee.....ee.....hhhhhhhhhhheeeeeeeee.hhh........eeeee...hhhhhhhhhhhh..eeee..........eeeeee.....hhhhhhhhhhh...eeee.ee......eeeee.....eeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kwm D   7 NNQDELKKLAATEAAKSITTEITLGVGTGSTVGFLIEELVNYRDKIKTVVSSSEDSTRKLKALGFDVVDLNYAGEIDLYIDGADECNNHKELIKGGGAALTREKICVAAAKKFICIIDESKKVNTLGNFPLPIEVIPMARSYIARQIVKLGGQPVYREQTITDNGNVILDVYNLKIDNPLKLETELNQITGVVTNGIFALKPADTVIMATKDSNIVVL 224
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216
   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 3KWM)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: ISOCOT_Fold (53)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RPIA_FRATT | Q5NFM5)
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: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.

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  5.3.1.6
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPIA_FRATT | Q5NFM5: 4io1

(-) Related Entries Specified in the PDB File

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