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(-) Description

Title :  STRUCTURE OF RIBOSE 5-PHOSPHATE ISOMERASE A FROM METHANOCALDOCOCCUS JANNASCHII
 
Authors :  S. V. Antonyuk, M. J. Ellis, R. W. Strange, S. S. Hasnain, Y. Bessho, S. Kuramitsu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  04 Sep 09  (Deposition) - 06 Oct 09  (Release) - 09 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Isomerase, Pentose Phosphate Pathway, Carbon Fixation, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Carbohydrate Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. W. Strange, S. V. Antonyuk, M. J. Ellis, Y. Bessho, S. Kuramitsu, S. Yokoyama, S. S. Hasnain
The Structure Of An Archaeal Ribose-5-Phosphate Isomerase From Methanocaldococcus Jannaschii (Mj1603).
Acta Crystallogr. , Sect. F V. 65 1214 2009
PubMed-ID: 20054114  |  Reference-DOI: 10.1107/S1744309109044923

(-) 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: PET-21A
    Expression System Strain: ROSETTA(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RPIA, MJ1603
    Organism Scientific: METHANOCALDOCOCCUS JANNASCHII
    Organism Taxid: 2190
    Strain: DSM2661
    Synonym: PHOSPHORIBOISOMERASE A, PRI

 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
1ACT1Ligand/IonACETATE ION
2CL4Ligand/IonCHLORIDE ION
3PGO11Ligand/IonS-1,2-PROPANEDIOL

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:98 , GLY A:100 , GLY A:101 , CYS A:102 , GLU A:106 , PGO A:233BINDING SITE FOR RESIDUE CL A 231
02AC2SOFTWAREARG A:37 , TYR A:66 , HOH A:249BINDING SITE FOR RESIDUE PGO A 234
03AC3SOFTWAREGLY A:29 , SER A:30 , THR A:31 , LYS A:124 , PGO A:233 , HOH A:243 , HOH A:290 , HOH A:340BINDING SITE FOR RESIDUE PGO A 232
04AC4SOFTWARETHR A:28 , ASP A:83 , GLY A:84 , ALA A:85 , ASP A:86 , LYS A:97 , GLY A:98 , GLU A:106 , CL A:231 , PGO A:232 , HOH A:371BINDING SITE FOR RESIDUE PGO A 233
05AC5SOFTWAREGLY B:98 , GLY B:100 , GLY B:101 , CYS B:102 , GLU B:106 , PGO B:233BINDING SITE FOR RESIDUE CL B 231
06AC6SOFTWAREALA B:85 , ASP B:86 , LYS B:97 , GLY B:98 , GLY B:99 , GLY B:100 , GLU B:106 , CL B:231 , PGO B:235 , HOH B:491 , HOH B:577 , HOH B:578BINDING SITE FOR RESIDUE PGO B 233
07AC7SOFTWARELEU B:70 , VAL B:71 , HOH B:450 , HOH B:470 , HOH B:494 , LEU D:70BINDING SITE FOR RESIDUE PGO B 234
08AC8SOFTWARELYS B:7 , GLY B:29 , SER B:30 , THR B:31 , LYS B:124 , PGO B:233 , HOH B:356 , HOH B:577BINDING SITE FOR RESIDUE PGO B 235
09AC9SOFTWAREGLY C:98 , GLY C:100 , GLY C:101 , CYS C:102 , GLU C:106 , PGO C:233BINDING SITE FOR RESIDUE CL C 231
10BC1SOFTWARETHR C:28 , ASP C:83 , GLY C:84 , ALA C:85 , ASP C:86 , LYS C:97 , GLY C:98 , GLY C:99 , GLY C:100 , GLU C:106 , CL C:231 , PGO C:234BINDING SITE FOR RESIDUE PGO C 233
11BC2SOFTWAREGLY C:29 , SER C:30 , THR C:31 , LYS C:124 , PGO C:233 , HOH C:248 , HOH C:249 , HOH C:282 , HOH C:289BINDING SITE FOR RESIDUE PGO C 234
12BC3SOFTWARELYS C:60 , HOH C:431BINDING SITE FOR RESIDUE ACT C 227
13BC4SOFTWAREGLY D:98 , GLY D:100 , GLY D:101 , CYS D:102 , GLU D:106 , PGO D:233BINDING SITE FOR RESIDUE CL D 231
14BC5SOFTWARELYS D:7 , GLY D:29 , SER D:30 , THR D:31 , LYS D:124 , PGO D:233 , HOH D:256BINDING SITE FOR RESIDUE PGO D 232
15BC6SOFTWARETHR D:28 , ASP D:83 , GLY D:84 , ALA D:85 , ASP D:86 , LYS D:97 , GLY D:98 , GLU D:106 , CL D:231 , PGO D:232BINDING SITE FOR RESIDUE PGO D 233
16BC7SOFTWAREGLU C:58 , LEU D:162 , GLY D:163 , LYS D:166 , ARG D:167 , GLY D:168BINDING SITE FOR RESIDUE PGO D 234

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3IXQ)

(-) 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:225
 aligned with RPIA_METJA | Q58998 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
           RPIA_METJA     2 SNEDLKLKVAKEAVKLVKDGMVIGLGTGSTAALFIRELGNRIREEELTVFGIPTSFEAKMLAMQYEIPLVTLDEYDVDIAFDGADEVEETTLFLIKGGGGCHTQEKIVDYNANEFVVLVDESKLVKKLGEKFPIPVEVIPSAYRVVIRALSEMGGEAVIRLGDRKRGPVITDNGNMIIDVFMNIDDAIELEKEINNIPGVVENGIFTKVDKVLVGTKKGVKTLKK 226
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------3ixqA02 A:128-205  [code=3.30.70.260, no name defined]                        --------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.............eeee...eee.....ee.....hhhhhhhhhhhh.eeeeeee...ee........eeeee...hhhhhhhhhhhh..eeee................eeeeee....hhhhhhhhhhh...eeee.ee....eeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ixq A   2 SNEDLKLKVAKEAVKLVKDGMVIGLGTGSTAALFIRELGNRIREEELTVFGIPTSFEAKMLAMQYEIPLVTLDEYDVDIAFDGADEVEETTLFLIKGGGGCHTQEKIVDYNANEFVVLVDESKLVKKLGEKFPIPVEVIPSAYRVVIRALSEMGGEAVIRLGDRKRGPVITDNGNMIIDVFMNIDDAIELEKEINNIPGVVENGIFTKVDKVLVGTKKGVKTLKK 226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with RPIA_METJA | Q58998 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
           RPIA_METJA     2 SNEDLKLKVAKEAVKLVKDGMVIGLGTGSTAALFIRELGNRIREEELTVFGIPTSFEAKMLAMQYEIPLVTLDEYDVDIAFDGADEVEETTLFLIKGGGGCHTQEKIVDYNANEFVVLVDESKLVKKLGEKFPIPVEVIPSAYRVVIRALSEMGGEAVIRLGDRKRGPVITDNGNMIIDVFMNIDDAIELEKEINNIPGVVENGIFTKVDKVLVGTKKGVKTLKK 226
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------3ixqB02 B:128-205  [code=3.30.70.260, no name defined]                        --------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.............eeee...eee.....ee.....hhhhhhhhhh...eeeeeee...ee........eeeee...hhhhhhhhhhhh..eeee................eeeeee....hhhhhhhhhhh...eeee.ee....eeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ixq B   2 SNEDLKLKVAKEAVKLVKDGMVIGLGTGSTAALFIRELGNRIREEELTVFGIPTSFEAKMLAMQYEIPLVTLDEYDVDIAFDGADEVEETTLFLIKGGGGCHTQEKIVDYNANEFVVLVDESKLVKKLGEKFPIPVEVIPSAYRVVIRALSEMGGEAVIRLGDRKRGPVITDNGNMIIDVFMNIDDAIELEKEINNIPGVVENGIFTKVDKVLVGTKKGVKTLKK 226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     


Chain C from PDB  Type:PROTEIN  Length:225
 aligned with RPIA_METJA | Q58998 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
           RPIA_METJA     2 SNEDLKLKVAKEAVKLVKDGMVIGLGTGSTAALFIRELGNRIREEELTVFGIPTSFEAKMLAMQYEIPLVTLDEYDVDIAFDGADEVEETTLFLIKGGGGCHTQEKIVDYNANEFVVLVDESKLVKKLGEKFPIPVEVIPSAYRVVIRALSEMGGEAVIRLGDRKRGPVITDNGNMIIDVFMNIDDAIELEKEINNIPGVVENGIFTKVDKVLVGTKKGVKTLKK 226
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------3ixqC02 C:128-205  [code=3.30.70.260, no name defined]                        --------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.............eeee...eee.....ee.....hhhhhhhhhhhh.eeeeeee...ee........eeeee...hhhhhhhhhhhh..eeee.ee....ee.......eeeeee....hhhhhhhhhhh...eeee.ee....eeeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ixq C   2 SNEDLKLKVAKEAVKLVKDGMVIGLGTGSTAALFIRELGNRIREEELTVFGIPTSFEAKMLAMQYEIPLVTLDEYDVDIAFDGADEVEETTLFLIKGGGGCHTQEKIVDYNANEFVVLVDESKLVKKLGEKFPIPVEVIPSAYRVVIRALSEMGGEAVIRLGDRKRGPVITDNGNMIIDVFMNIDDAIELEKEINNIPGVVENGIFTKVDKVLVGTKKGVKTLKK 226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     


Chain D from PDB  Type:PROTEIN  Length:225
 aligned with RPIA_METJA | Q58998 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:225
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221     
           RPIA_METJA     2 SNEDLKLKVAKEAVKLVKDGMVIGLGTGSTAALFIRELGNRIREEELTVFGIPTSFEAKMLAMQYEIPLVTLDEYDVDIAFDGADEVEETTLFLIKGGGGCHTQEKIVDYNANEFVVLVDESKLVKKLGEKFPIPVEVIPSAYRVVIRALSEMGGEAVIRLGDRKRGPVITDNGNMIIDVFMNIDDAIELEKEINNIPGVVENGIFTKVDKVLVGTKKGVKTLKK 226
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------3ixqD02 D:128-205  [code=3.30.70.260, no name defined]                        --------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh.............eeee...eee.....ee.....hhhhhhhhhh...eeeeeee...ee........eeeee...hhhhhhhhhhhh..eeee................eeeeee....hhhhhhhhhhh...eeee.ee....eeeee....eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ixq D   2 SNEDLKLKVAKEAVKLVKDGMVIGLGTGSTAALFIRELGNRIREEELTVFGIPTSFEAKMLAMQYEIPLVTLDEYDVDIAFDGADEVEETTLFLIKGGGGCHTQEKIVDYNANEFVVLVDESKLVKKLGEKFPIPVEVIPSAYRVVIRALSEMGGEAVIRLGDRKRGPVITDNGNMIIDVFMNIDDAIELEKEINNIPGVVENGIFTKVDKVLVGTKKGVKTLKK 226
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   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  (0, 0)

(no "SCOP Domain" information available for 3IXQ)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RPIA_METJA | Q58998)
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: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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