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(-) Description

Title :  STRUCTURE OF D-RIBOSE-5-PHOSPHATE ISOMERASE FROM IN COMPLEX WITH PHOSPHO-ERYTHRONIC ACID
 
Authors :  K. Ishikawa, I. Matsui, F. Payan, C. Cambillau, H. Ishida, Y. Kawarabayasi, H. Kikuchi, A. Roussel
Date :  24 Apr 02  (Deposition) - 03 Jul 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha/Beta Structure, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ishikawa, I. Matsui, F. Payan, C. Cambillau, H. Ishida, Y. Kawarabayasi, H. Kikuchi, A. Roussel
A Hyperthermostable D-Ribose-5-Phosphate Isomerase From Pyrococcus Horikoshii Characterization And Three-Dimensional Structure
Structure V. 10 877 2002
PubMed-ID: 12057201  |  Reference-DOI: 10.1016/S0969-2126(02)00779-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - D-RIBOSE-5-PHOSPHATE ISOMERASE
    Chains: A, B, C, D
    EC Number: 5.3.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1CL10Ligand/IonCHLORIDE ION
2DER4Ligand/IonD-4-PHOSPHOERYTHRONIC ACID
3NA2Ligand/IonSODIUM ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:99 , GLY A:101 , ALA A:102 , ALA A:103 , GLU A:107 , DER A:1001BINDING SITE FOR RESIDUE CL A 2001
02AC2SOFTWAREGLY B:99 , GLY B:101 , ALA B:102 , ALA B:103 , GLU B:107 , DER B:1002BINDING SITE FOR RESIDUE CL B 2002
03AC3SOFTWAREGLY C:99 , GLY C:101 , ALA C:102 , ALA C:103 , GLU C:107 , DER C:1003BINDING SITE FOR RESIDUE CL C 2003
04AC4SOFTWAREGLY D:99 , GLY D:101 , ALA D:102 , ALA D:103 , GLU D:107 , DER D:1004BINDING SITE FOR RESIDUE CL D 2004
05AC5SOFTWARESER A:57 , TYR A:58 , GLN A:59 , ASP A:174 , LYS C:167 , ASP C:168 , GLY C:169BINDING SITE FOR RESIDUE CL A 2005
06AC6SOFTWARESER B:57 , TYR B:58 , GLN B:59 , ASP B:174 , HOH B:2036 , LYS D:167 , ASP D:168 , GLY D:169BINDING SITE FOR RESIDUE CL B 2006
07AC7SOFTWARELYS A:167 , ASP A:168 , GLY A:169 , SER C:57 , TYR C:58 , GLN C:59 , ASP C:174BINDING SITE FOR RESIDUE CL C 2007
08AC8SOFTWARELYS B:167 , ASP B:168 , SER D:57 , TYR D:58 , GLN D:59 , ASP D:174BINDING SITE FOR RESIDUE CL D 2008
09AC9SOFTWAREVAL A:165 , ASN A:166 , VAL C:165 , ASN C:166BINDING SITE FOR RESIDUE CL A 2009
10BC1SOFTWAREVAL B:165 , ASN B:166 , VAL D:165 , ASN D:166BINDING SITE FOR RESIDUE CL B 2010
11BC2SOFTWAREASN A:175 , HOH A:2019 , HOH A:2049 , HOH A:2050 , ASN B:175 , HOH B:2026BINDING SITE FOR RESIDUE NA A 2011
12BC3SOFTWAREASN C:175 , HOH C:2051 , HOH C:2052 , ASN D:175 , HOH D:2039 , HOH D:2040BINDING SITE FOR RESIDUE NA C 2012
13BC4SOFTWARETHR A:28 , SER A:30 , THR A:31 , ASP A:85 , GLY A:86 , ALA A:87 , ASP A:88 , LYS A:98 , GLY A:99 , ARG A:100 , GLY A:101 , GLU A:107 , LYS A:125 , CL A:2001 , HOH A:2052 , HOH A:2053 , HOH A:2098BINDING SITE FOR RESIDUE DER A 1001
14BC5SOFTWARETHR B:28 , SER B:30 , THR B:31 , ASP B:85 , GLY B:86 , ALA B:87 , ASP B:88 , LYS B:98 , GLY B:99 , GLY B:101 , GLU B:107 , LYS B:125 , CL B:2002 , HOH B:2031 , HOH B:2038 , HOH D:2082BINDING SITE FOR RESIDUE DER B 1002
15BC6SOFTWARETHR C:28 , GLY C:29 , SER C:30 , THR C:31 , ASP C:85 , GLY C:86 , ALA C:87 , ASP C:88 , LYS C:98 , GLY C:99 , ARG C:100 , GLY C:101 , GLU C:107 , LYS C:125 , CL C:2003 , HOH C:2020 , HOH C:2055 , HOH C:2059 , HOH C:2074 , HOH C:2100BINDING SITE FOR RESIDUE DER C 1003
16BC7SOFTWARETHR D:28 , SER D:30 , THR D:31 , ASP D:85 , GLY D:86 , ALA D:87 , ASP D:88 , LYS D:98 , GLY D:99 , GLY D:101 , GLU D:107 , LYS D:125 , CL D:2004 , HOH D:2035 , HOH D:2054 , HOH D:2055 , HOH D:2105BINDING SITE FOR RESIDUE DER D 1004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LK7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LK7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LK7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LK7)

(-) Exons   (0, 0)

(no "Exon" information available for 1LK7)

(-) 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:229
 aligned with RPIA_PYRHO | O50083 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
           RPIA_PYRHO     1 MNVEEMKKIAAKEALKFIEDDMVIGLGTGSTTAYFIKLLGEKLKRGEISDIVGVPTSYQAKLLAIEHDIPIASLDQVDAIDVAVDGADEVDPNLNLIKGRGAALTMEKIIEYRAGTFIVLVDERKLVDYLCQKMPVPIEVIPQAWKAIIEELSIFNAKAELRMGVNKDGPVITDNGNFIIDAKFPRIDDPLDMEIELNTIPGVIENGIFADIADIVIVGTREGVKKLER 229
               SCOP domains d1lk7a1 A:1-130,A:211-229 D-ribose-5-phosphate isomerase (RpiA), catalytic domain                                                 d1lk7a2 A:131-210 D-ribose-5-phosphate isomerase (RpiA), lid domain             d1lk7a1             SCOP domains
               CATH domains 1lk7A01 A:1-128,A:208-229  [code=3.40.50.1360, no name defined]                                                                 1lk7A02 A:129-207  [code=3.30.70.260, no name defined]                         1lk7A01                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhh.....hhhhh..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
                 1lk7 A   1 MNVEEMKKIAAKEALKFIEDDMVIGLGTGSTTAYFIKLLGEKLKRGEISDIVGVPTSYQAKLLAIEHDIPIASLDQVDAIDVAVDGADEVDPNLNLIKGRGAALTMEKIIEYRAGTFIVLVDERKLVDYLCQKMPVPIEVIPQAWKAIIEELSIFNAKAELRMGVNKDGPVITDNGNFIIDAKFPRIDDPLDMEIELNTIPGVIENGIFADIADIVIVGTREGVKKLER 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         


Chain B from PDB  Type:PROTEIN  Length:229
 aligned with RPIA_PYRHO | O50083 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
           RPIA_PYRHO     1 MNVEEMKKIAAKEALKFIEDDMVIGLGTGSTTAYFIKLLGEKLKRGEISDIVGVPTSYQAKLLAIEHDIPIASLDQVDAIDVAVDGADEVDPNLNLIKGRGAALTMEKIIEYRAGTFIVLVDERKLVDYLCQKMPVPIEVIPQAWKAIIEELSIFNAKAELRMGVNKDGPVITDNGNFIIDAKFPRIDDPLDMEIELNTIPGVIENGIFADIADIVIVGTREGVKKLER 229
               SCOP domains d1lk7b1 B:1-130,B:211-229 D-ribose-5-phosphate isomerase (RpiA), catalytic domain                                                 d1lk7b2 B:131-210 D-ribose-5-phosphate isomerase (RpiA), lid domain             d1lk7b1             SCOP domains
               CATH domains 1lk7B01 B:1-128,B:208-229  [code=3.40.50.1360, no name defined]                                                                 1lk7B02 B:129-207  [code=3.30.70.260, no name defined]                         1lk7B01                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhh.....hhhhh..eeeeee...ee.....ee.....hhhhhhhhhh.eeeeeeeee.hhh.........eeeee...hhhhhhhhhhh...eeee................eeeeee.....hhhhhhhhhhhh..eeee.ee.....eeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lk7 B   1 MNVEEMKKIAAKEALKFIEDDMVIGLGTGSTTAYFIKLLGEKLKRGEISDIVGVPTSYQAKLLAIEHDIPIASLDQVDAIDVAVDGADEVDPNLNLIKGRGAALTMEKIIEYRAGTFIVLVDERKLVDYLCQKMPVPIEVIPQAWKAIIEELSIFNAKAELRMGVNKDGPVITDNGNFIIDAKFPRIDDPLDMEIELNTIPGVIENGIFADIADIVIVGTREGVKKLER 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         


Chain C from PDB  Type:PROTEIN  Length:229
 aligned with RPIA_PYRHO | O50083 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
           RPIA_PYRHO     1 MNVEEMKKIAAKEALKFIEDDMVIGLGTGSTTAYFIKLLGEKLKRGEISDIVGVPTSYQAKLLAIEHDIPIASLDQVDAIDVAVDGADEVDPNLNLIKGRGAALTMEKIIEYRAGTFIVLVDERKLVDYLCQKMPVPIEVIPQAWKAIIEELSIFNAKAELRMGVNKDGPVITDNGNFIIDAKFPRIDDPLDMEIELNTIPGVIENGIFADIADIVIVGTREGVKKLER 229
               SCOP domains d1lk7c1 C:1-130,C:211-229 D-ribose-5-phosphate isomerase (RpiA), catalytic domain                                                 d1lk7c2 C:131-210 D-ribose-5-phosphate isomerase (RpiA), lid domain             d1lk7c1             SCOP domains
               CATH domains 1lk7C01 C:1-128,C:208-229  [code=3.40.50.1360, no name defined]                                                                 1lk7C02 C:129-207  [code=3.30.70.260, no name defined]                         1lk7C01                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh......eeee.hhhhhhhhhhh.....hhhhh..eeeeee...ee.....ee.....hhhhhhhhhh.eeeeeeeee.hhh.........eeeee...hhhhhhhhhhhh..eeee................eeeeee.....hhhhhhhhhh....eeee.ee.....eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lk7 C   1 MNVEEMKKIAAKEALKFIEDDMVIGLGTGSTTAYFIKLLGEKLKRGEISDIVGVPTSYQAKLLAIEHDIPIASLDQVDAIDVAVDGADEVDPNLNLIKGRGAALTMEKIIEYRAGTFIVLVDERKLVDYLCQKMPVPIEVIPQAWKAIIEELSIFNAKAELRMGVNKDGPVITDNGNFIIDAKFPRIDDPLDMEIELNTIPGVIENGIFADIADIVIVGTREGVKKLER 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         


Chain D from PDB  Type:PROTEIN  Length:229
 aligned with RPIA_PYRHO | O50083 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
           RPIA_PYRHO     1 MNVEEMKKIAAKEALKFIEDDMVIGLGTGSTTAYFIKLLGEKLKRGEISDIVGVPTSYQAKLLAIEHDIPIASLDQVDAIDVAVDGADEVDPNLNLIKGRGAALTMEKIIEYRAGTFIVLVDERKLVDYLCQKMPVPIEVIPQAWKAIIEELSIFNAKAELRMGVNKDGPVITDNGNFIIDAKFPRIDDPLDMEIELNTIPGVIENGIFADIADIVIVGTREGVKKLER 229
               SCOP domains d1lk7d1 D:1-130,D:211-229 D-ribose-5-phosphate isomerase (RpiA), catalytic domain                                                 d1lk7d2 D:131-210 D-ribose-5-phosphate isomerase (RpiA), lid domain             d1lk7d1             SCOP domains
               CATH domains 1lk7D01 D:1-128,D:208-229  [code=3.40.50.1360, no name defined]                                                                 1lk7D02 D:129-207  [code=3.30.70.260, no name defined]                         1lk7D01                CATH domains
           Pfam domains (1) --------------------------------------------------Rib_5-P_isom_A-1lk7D01 D:51-225                                                                                                                                                ---- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------Rib_5-P_isom_A-1lk7D02 D:51-225                                                                                                                                                ---- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------Rib_5-P_isom_A-1lk7D03 D:51-225                                                                                                                                                ---- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------Rib_5-P_isom_A-1lk7D04 D:51-225                                                                                                                                                ---- Pfam domains (4)
         Sec.struct. author .hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhh.....hhhhh..eeeeee...ee.....ee.....hhhhhhhhhh.eeeeeeeee.hhh.........eeeee...hhhhhhhhhhhhh.eeee................eeeeee.....hhhhhhhhhhh...eeee.ee.....eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lk7 D   1 MNVEEMKKIAAKEALKFIEDDMVIGLGTGSTTAYFIKLLGEKLKRGEISDIVGVPTSYQAKLLAIEHDIPIASLDQVDAIDVAVDGADEVDPNLNLIKGRGAALTMEKIIEYRAGTFIVLVDERKLVDYLCQKMPVPIEVIPQAWKAIIEELSIFNAKAELRMGVNKDGPVITDNGNFIIDAKFPRIDDPLDMEIELNTIPGVIENGIFADIADIVIVGTREGVKKLER 229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
   Legend:   → Mismatch (orange background)
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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  (2, 8)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RPIA_PYRHO | O50083)
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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  1lk7
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  RPIA_PYRHO | O50083
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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_PYRHO | O50083: 1lk5

(-) Related Entries Specified in the PDB File

1lk5 1LK5 CONTAINS THE SAME PROTEIN WITHOUT LIGAND