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(-) Description

Title :  CRYSTAL STRUCTURE OF A PUTATIVE RIBOSE-5-PHOSPHATE ISOMERASE FROM COCCIDIOIDES IMMITIS SOLVED BY COMBINED IODIDE ION SAD AND MR
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  17 Jan 11  (Deposition) - 09 Feb 11  (Release) - 26 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Ssgcid, Coccidioidomycosis, Putative Uncharacterized Protein, Hypothetical Protein, Ribose-5-Phosphate Isomerase, Iodide Ion, Isomerase (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 - PUTATIVE RIBOSE-5-PHOSPHATE ISOMERASE
    Chains: A, B
    EC Number: 5.3.1.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: AVA0421
    Gene: CIMG_07932, 4559626
    Organism Scientific: COCCIDIOIDES IMMITIS
    Organism Taxid: 246410
    Strain: RS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 33)

Asymmetric Unit (3, 33)
No.NameCountTypeFull Name
1CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3IOD29Ligand/IonIODIDE ION
Biological Unit 1 (3, 33)
No.NameCountTypeFull Name
1CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3IOD29Ligand/IonIODIDE ION
Biological Unit 2 (3, 66)
No.NameCountTypeFull Name
1CSO4Mod. Amino AcidS-HYDROXYCYSTEINE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3IOD58Ligand/IonIODIDE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:71 , ASP A:111 , ALA A:112 , HOH A:205 , HOH A:256BINDING SITE FOR RESIDUE EDO A 164
02AC2SOFTWAREARG B:71 , ASP B:111 , ALA B:112 , HOH B:212 , HOH B:264BINDING SITE FOR RESIDUE EDO B 164
03AC3SOFTWAREIOD A:166 , HOH A:241BINDING SITE FOR RESIDUE IOD A 165
04AC4SOFTWAREIOD A:165BINDING SITE FOR RESIDUE IOD A 166
05AC5SOFTWAREIOD A:168 , HOH B:182BINDING SITE FOR RESIDUE IOD A 167
06AC6SOFTWAREARG A:138 , IOD A:167BINDING SITE FOR RESIDUE IOD A 168
07AC7SOFTWARECSO A:76 , THR A:78 , GLY A:81 , HOH A:195BINDING SITE FOR RESIDUE IOD A 169
08AC8SOFTWAREIOD A:171BINDING SITE FOR RESIDUE IOD A 170
09AC9SOFTWAREGLY A:77 , ARG A:120 , IOD A:170 , HOH A:278BINDING SITE FOR RESIDUE IOD A 171
10BC1SOFTWAREALA A:52 , ALA B:151BINDING SITE FOR RESIDUE IOD A 174
11BC2SOFTWAREGLN A:62 , TYR B:155BINDING SITE FOR RESIDUE IOD A 175
12BC3SOFTWAREASP A:99 , THR A:100BINDING SITE FOR RESIDUE IOD A 176
13BC4SOFTWAREHOH A:243 , ARG B:120BINDING SITE FOR RESIDUE IOD B 165
14BC5SOFTWAREIOD B:180BINDING SITE FOR RESIDUE IOD B 166
15BC6SOFTWARETYR A:155 , SER B:46 , HOH B:202 , HOH B:214BINDING SITE FOR RESIDUE IOD B 172
16BC7SOFTWAREALA B:52 , HIS B:55BINDING SITE FOR RESIDUE IOD B 174
17BC8SOFTWAREASP B:99 , THR B:100BINDING SITE FOR RESIDUE IOD B 175
18BC9SOFTWAREHIS B:29 , HOH B:253 , HOH B:255BINDING SITE FOR RESIDUE IOD B 176
19CC1SOFTWAREGLN B:141 , LYS B:142BINDING SITE FOR RESIDUE IOD B 177
20CC2SOFTWAREHOH B:191BINDING SITE FOR RESIDUE IOD B 179
21CC3SOFTWAREIOD B:166 , HOH B:197BINDING SITE FOR RESIDUE IOD B 180

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QD5)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:43 -Val A:44
2Gly B:43 -Val B:44

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3QD5)

(-) Exons   (0, 0)

(no "Exon" information available for 3QD5)

(-) 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:160
 aligned with RPIB_COCIM | P0CL19 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:160
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
           RPIB_COCIM     3 ATPLPPLRLAIACDDAGVSYKEALKAHLSDNPLVSSITDVGVTSTTDKTAYPHVAIQAAQLIKDGKVDRALMICGTGLGVAISANKVPGIRAVTAHDTFSVERAILSNDAQVLCFGQRVIGIELAKRLAGEWLTYRFDQKSASAQKVQAISDYEKKFVEV 162
               SCOP domains d3qd5a_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...hhhhhhhhhhhhhh...eeeeeeee........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhh....eeeee....hhhhhhhhhhhhh.......hhhhhhhhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qd5 A   3 ATPLPPLRLAIACDDAGVSYKEALKAHLSDNPLVSSITDVGVTSTTDKTAYPHVAIQAAQLIKDGKVDRALMIcGTGLGVAISANKVPGIRAVTAHDTFSVERAILSNDAQVLCFGQRVIGIELAKRLAGEWLTYRFDQKSASAQKVQAISDYEKKFVEV 162
                                    12        22        32        42        52        62        72   |    82        92       102       112       122       132       142       152       162
                                                                                                    76-CSO                                                                                  


Chain B from PDB  Type:PROTEIN  Length:160
 aligned with RPIB_COCIM | P0CL19 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:160
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163
           RPIB_COCIM     4 TPLPPLRLAIACDDAGVSYKEALKAHLSDNPLVSSITDVGVTSTTDKTAYPHVAIQAAQLIKDGKVDRALMICGTGLGVAISANKVPGIRAVTAHDTFSVERAILSNDAQVLCFGQRVIGIELAKRLAGEWLTYRFDQKSASAQKVQAISDYEKKFVEVN 163
               SCOP domains d3qd5b_ B: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee...hhhhhhhhhhhhhh...eeeeee..........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhh....eeeee....hhhhhhhhhhhhh........hhhhhhhhhhhhhh.eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qd5 B   4 TPLPPLRLAIACDDAGVSYKEALKAHLSDNPLVSSITDVGVTSTTDKTAYPHVAIQAAQLIKDGKVDRALMIcGTGLGVAISANKVPGIRAVTAHDTFSVERAILSNDAQVLCFGQRVIGIELAKRLAGEWLTYRFDQKSASAQKVQAISDYEKKFVEVN 163
                                    13        23        33        43        53        63        73  |     83        93       103       113       123       133       143       153       163
                                                                                                   76-CSO
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QD5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QD5)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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        RPIB_COCIM | P0CL19: 3sdw 3sgw

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