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(-) Description

Title :  CRYSTAL STRUCTURE OF A RIBOSE 5-PHOSPHATE ISOMERASE RPIB (TM1080) FROM THERMOTOGA MARITIMA AT 1.90 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  12 Feb 03  (Deposition) - 01 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xu, R. Schwarzenbacher, D. Mcmullan, F. Von Delft, L. S. Brinen, J. M. Canaves, X. Dai, A. M. Deacon, M. A. Elsliger, S. Eshagi, R. Floyd, A. Godzik, C. Grittini, S. K. Grzechnik, L. Jaroszewski, C. Karlak, H. E. Klock, E. Koesema, J. S. Kovarik, A. Kreusch, P. Kuhn, S. A. Lesley I. Levin, T. M. Mcphillips, M. D. Miller, A. Morse, K. Moy, J. Ouyang, R. Page, K. Quijano, A. Robb, G. Spraggon, F. Stevens, H. Van Den Bedem, J. Velasquez, J. Vincent, X. Wang, B. West, G. Wolf, K. O. Hodgson, J. Wooley, I. A. Wilson
Crystal Structure Of A Ribose-5-Phosphate Isomerase Rpib (Tm1080) From Thermotoga Maritima At 1. 90 A Resolution.
Proteins V. 56 171 2004
PubMed-ID: 15162497  |  Reference-DOI: 10.1002/PROT.20129

(-) Compounds

Molecule 1 - RIBOSE-5-PHOSPHATE ISOMERASE RPIB
    Chains: A
    EC Number: 5.3.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM1080
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE2Mod. Amino AcidSELENOMETHIONINE
3OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MSE8Mod. Amino AcidSELENOMETHIONINE
3OCS4Mod. Amino AcidCYSTEINESULFONIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:87 , PHE A:88 , ILE A:111BINDING SITE FOR RESIDUE MPD A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1O1X)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:33 -Thr A:34

 Sequence-Structure Mapping

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(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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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:145
 aligned with Q9X0G9_THEMA | Q9X0G9 from UniProtKB/TrEMBL  Length:143

    Alignment length:145
                              1                                                                                                                                              
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138     
         Q9X0G9_THEMA     - --MKIAIASDHAAFELKEKVKNYLLGKGIEVEDHGTYSEESVDYPDYAKKVVQSILSNEADFGILLCGTGLGMSIAANRYRGIRAALCLFPDMARLARSHNNANILVLPGRLIGAELAFWIVDTFLSTPFDGGRHERRIRKIDEV 143
               SCOP domains d1o1xa_ A: Putative sugar-phosphate isomerase                                                                                                     SCOP domains
               CATH domains 1o1xA00 A:-1-143  [code=3.40.1400.10, no name defined]                                                                                            CATH domains
               Pfam domains ---LacAB_rpiB-1o1xA01 A:2-141                                                                                                                  -- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhh......eee..hhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh.....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1o1x A  -1 HHVKIAIASDHAAFELKEKVKNYLLGKGIEVEDHGTYSEESVDYPDYAKKVVQSILSNEADFGILLcGTGLGmSIAANRYRGIRAALCLFPDmARLARSHNNANILVLPGRLIGAELAFWIVDTFLSTPFDGGRHERRIRKIDEV 143
                                     8        18        28        38        48        58      | 68  |     78        88  |     98       108       118       128       138     
                                                                                             65-OCS |                  91-MSE                                                
                                                                                                   71-MSE
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: LacAB_rpiB] (12)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q9X0G9_THEMA | Q9X0G9)
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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