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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOSE-5-PHOSPHATE ISOMERASE LACAB_RPIB FROM VIBRIO PARAHAEMOLYTICUS
 
Authors :  Y. Kim, L. Volkart, J. Abdullah, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  30 Aug 10  (Deposition) - 08 Sep 10  (Release) - 08 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Alpha-Beta-Alpha Sandwich, Cytosol, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, L. Volkart, J. Abdullah, A. Joachimiak
Crystal Structure Of Ribose-5-Phosphate Isomerase Lacab_rpi From Vibrio Parahaemolyticus
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RIBOSE/GALACTOSE ISOMERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: VPA0080
    Organism Scientific: VIBRIO PARAHAEMOLYTICUS
    Organism Taxid: 223926
    Strain: RIMD 2210633
    Synonym: PUTATIVE SUGAR-PHOSPHATE ISOMERASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MSE7Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 32)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MSE28Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:86 , ASN A:106 , GLY A:107 , ASN A:108 , ASN A:158 , HOH A:237 , HOH A:240BINDING SITE FOR RESIDUE GOL A 215

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:142 -Pro A:143

 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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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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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:212
 aligned with Q87K18_VIBPA | Q87K18 from UniProtKB/TrEMBL  Length:211

    Alignment length:212
                              1                                                                                                                                                                                                                 
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208  
         Q87K18_VIBPA     - --MKIALMMENSQAAKNAMVAGELNSVAGGLGHDVFNVGMTDENDHHLTYIHLGIMASILLNSKAVDFVVTGCGTGQGALMSCNLHPGVVCGYCLEPSDAFLFNQINNGNAISLAFAKGFGWAGELNVRYIFEKAFTGKRGEGYPIERAAPQQANAAILNNVKAAVAKDVVEGLRAIDQELVKTAVGSTQFQECFFAHCQVPEIAEYVKSLL 210
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---LacAB_rpiB-3onoA02 A:2-161                                                                                                                                      DUF3666-3onoA01 A:162-209                       - Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhhhhhhhhh..eeee...........hhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhh.....eee..hhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ono A  -1 NAmKIALmmENSQAAKNAmVAGELNSVAGGLGHDVFNVGmTDENDHHLTYIHLGImASILLNSKAVDFVVTGCGTGQGALmSCNLHPGVVCGYCLEPSDAFLFNQINNGNAISLAFAKGFGWAGELNVRYIFEKAFTGKRGEGYPIERAAPQQANAAILNNVKAAVAKDVVEGLRAIDQELVKTAVGSTQFQECFFAHCQVPEIAEYVKSLL 210
                              |    ||8        18        28        38        48     |  58        68        78|       88        98       108       118       128       138       148       158       168       178       188       198       208  
                              |    ||        17-MSE               38-MSE          54-MSE                   79-MSE                                                                                                                               
                              1-MSE||                                                                                                                                                                                                           
                                   6-MSE                                                                                                                                                                                                        
                                    7-MSE
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: DUF3666] (1)
(-)
Clan: no clan defined [family: LacAB_rpiB] (12)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q87K18_VIBPA | Q87K18)
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.
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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