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(-) Description

Title :  CRYSTAL STRUCTURE OF A RIBOSE-5-PHOSPHATE ISOMERASE B RPIB FROM COCCIDIOIDES IMMITIS BOUND TO PHOSPHATE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 Jun 11  (Deposition) - 22 Jun 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (4x)
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Ribose-5-Phosphate, Rpib, Valley Fever, Coccidioidomycosis, Pathogenic Fungus, Dust-Borne Pathogen, Isomerase, Nucleotide And Co-Factor Biogenesis, Pentose Phosphate Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. E. Edwards, A. B. Abramov, E. R. Smith, R. O. Baydo, J. T. Leonard, D. J. Leibly, K. B. Thompkins, M. C. Clifton, A. S. Gardberg, B. L. Staker, W. C. Van Voorhis, P. J. Myler, L. J. Stewart
Structural Characterization Of A Ribose-5-Phosphate Isomerase B From The Pathogenic Fungus Coccidioides Immitis
Bmc Struct. Biol. V. 11 39 2011
PubMed-ID: 21995815  |  Reference-DOI: 10.1186/1472-6807-11-39

(-) Compounds

Molecule 1 - RIBOSE 5-PHOSPHATE ISOMERASE
    Chains: A
    EC Number: 5.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PAVA0421
    Gene: CIMG_07932
    Organism Common: VALLEY FEVER FUNGUS
    Organism Scientific: COCCIDIOIDES IMMITIS
    Organism Taxid: 246410
    Strain: RS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A
Biological Unit 2 (2x): A
Biological Unit 3 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3PO42Ligand/IonPHOSPHATE ION
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO8Ligand/Ion1,2-ETHANEDIOL
3PO44Ligand/IonPHOSPHATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:53 , SER A:109 , SER A:145 , LYS A:148 , HOH A:171 , HOH A:315BINDING SITE FOR RESIDUE PO4 A 164
2AC2SOFTWAREARG A:71 , ASP A:111 , ALA A:112 , HOH A:191 , HOH A:251BINDING SITE FOR RESIDUE EDO A 165
3AC3SOFTWARELYS A:88 , HOH A:209BINDING SITE FOR RESIDUE EDO A 166
4AC4SOFTWAREASP A:99 , THR A:100BINDING SITE FOR RESIDUE CL A 167

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:43 -Val A:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SDW)

(-) 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:158
 aligned with RPIB_COCIM | P0CL19 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:158
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155        
           RPIB_COCIM     6 LPPLRLAIACDDAGVSYKEALKAHLSDNPLVSSITDVGVTSTTDKTAYPHVAIQAAQLIKDGKVDRALMICGTGLGVAISANKVPGIRAVTAHDTFSVERAILSNDAQVLCFGQRVIGIELAKRLAGEWLTYRFDQKSASAQKVQAISDYEKKFVEVN 163
               SCOP domains d3sdwa_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----LacAB_rpiB-3sdwA01 A:10-153                                                                                                                     ---------- Pfam domains
         Sec.struct. author ...eeeeeee...hhhhhhhhhhhhh....eeeeee..........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sdw A   6 LPPLRLAIACDDAGVSYKEALKAHLSDNPLVSSITDVGVTSTTDKTAYPHVAIQAAQLIKDGKVDRALMICGTGLGVAISANKVPGIRAVTAHDTFSVERAILSNDAQVLCFGQRVIGIELAKRLAGEWLTYRFDQKSASAQKVQAISDYEKKFVEVN 163
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155
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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  (0, 0)

(no "CATH Domain" information available for 3SDW)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (RPIB_COCIM | P0CL19)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RPIB_COCIM | P0CL19: 3qd5 3sgw

(-) Related Entries Specified in the PDB File

3qd5 SAME PROTEIN SOLVED BY IODIDE ION SAD PHASING WITH OXIDIZED CYSTEINE RESIDUE IN ACTIVE SITE
3s5p RPIB FROM GIARDIA LAMBLIA RELATED ID: COIMA.00584.A RELATED DB: TARGETDB