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(-) Description

Title :  METAL-FREE FORM OF PSEUDOMONAS STUTZERI L-RHAMNOSE ISOMERASE
 
Authors :  H. Yoshida, M. Yamaji, T. Ishii, K. Izumori, S. Kamitori
Date :  28 Aug 09  (Deposition) - 02 Feb 10  (Release) - 02 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta/Alpha Barrel, Homo-Tetramer, Metal-Binding Protein, Tim Barrel, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Yoshida, M. Yamaji, T. Ishii, K. Izumori, S. Kamitori
Catalytic Reaction Mechanism Of Pseudomonas Stutzeri L-Rhamnose Isomerase Deduced From X-Ray Structures
Febs J. V. 277 1045 2010
PubMed-ID: 20088877  |  Reference-DOI: 10.1111/J.1742-4658.2009.07548.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - L-RHAMNOSE ISOMERASE
    Chains: A, B, C, D
    EC Number: 5.3.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: PSEUDOMONAS PERFECTOMARINA
    Organism Scientific: PSEUDOMONAS STUTZERI
    Organism Taxid: 316

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3ITY)

(-) Sites  (0, 0)

(no "Site" information available for 3ITY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ile A:102 -Pro A:103
2Glu A:224 -Pro A:225
3Ile B:102 -Pro B:103
4Glu B:224 -Pro B:225
5Ile C:102 -Pro C:103
6Glu C:224 -Pro C:225
7Ile D:102 -Pro D:103
8Glu D:224 -Pro D:225

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ITY)

(-) 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:421
 aligned with Q75WH8_PSEST | Q75WH8 from UniProtKB/TrEMBL  Length:430

    Alignment length:421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
         Q75WH8_PSEST     4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASVA 424
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....ee.hhh.................hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhh.ee..ee......................hhhhhhhhhhhhhhhhhhhhhhh..eeee....ee......hhhhhhhhhhhhhhhhhhh.....eeeee.........ee...hhhhhhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhhh.........ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ity A   4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTNAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASVA 424
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 


Chain B from PDB  Type:PROTEIN  Length:421
 aligned with Q75WH8_PSEST | Q75WH8 from UniProtKB/TrEMBL  Length:430

    Alignment length:421
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 
         Q75WH8_PSEST     4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASVA 424
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....ee.hhhh...............hhhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhh.ee..ee......................hhhhhhhhhhhhhhhhhhhhhh...eeee....ee......hhhhhhhhhhhhhhhhhhh.....eeeee.........ee...hhhhhhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhhhh........ee.......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ity B   4 FRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTNAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASVA 424
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423 


Chain C from PDB  Type:PROTEIN  Length:428
 aligned with Q75WH8_PSEST | Q75WH8 from UniProtKB/TrEMBL  Length:430

    Alignment length:428
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422        
         Q75WH8_PSEST     3 EFRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASVAGGGGII 430
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....ee.hhhh................hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhh.ee..ee......................hhhhhhhhhhhhhhhhhhhhhhh..eeee....ee......hhhhhhhhhhhhhhhhhhh.....eeeee.........ee...hhhhhhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhhh.........ee.......hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ity C   3 EFRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTNAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPASVAGGGGII 430
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422        


Chain D from PDB  Type:PROTEIN  Length:419
 aligned with Q75WH8_PSEST | Q75WH8 from UniProtKB/TrEMBL  Length:430

    Alignment length:419
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412         
         Q75WH8_PSEST     3 EFRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTDAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPA 421
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....ee.hhh.................hhhhhhhhhhhhhhhhh...eee........hhhhhhhhhhhhh.ee..ee......................hhhhhhhhhhhhhhhhhhhhhhh..eeee....ee......hhhhhhhhhhhhhhhhhhh.....eeeee.........ee...hhhhhhhhhhhhh..eeeeee.hhh....hhhhhhhhhhhh..eeeeee...............hhhhhhhhhhhhhhhhhh.........ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ity D   3 EFRIAQDVVARENDRRASALKEDYEALGANLARRGVDIEAVTAKVEKFFVAVPSWGVGTGGTRFARFPGTGEPRGIFDKLDDCAVIQQLTRATPNVSLHIPWDKADPKELKARGDALGLGFDAMNSNTFSDAPGQAHSYKYGSLSHTNAATRAQAVEHNLECIEIGKAIGSKALTVWIGDGSNFPGQSNFTRAFERYLSAMAEIYKGLPDDWKLFSEHKMYEPAFYSTVVQDWGTNYLIAQTLGPKAQCLVDLGHHAPNTNIEMIVARLIQFGKLGGFHFNDSKYGDDDLDAGAIEPYRLFLVFNELVDAEARGVKGFHPAHMIDQSHNVTDPIESLINSANEIRRAYAQALLVDRAALSGYQEDNDALMATETLKRAYRTDVEPILAEARRRTGGAVDPVATYRASGYRARVAAERPA 421
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q75WH8_PSEST | Q75WH8)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  Cis Peptide Bonds
    Glu A:224 - Pro A:225   [ RasMol ]  
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  5.3.1.14
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 Related Entries

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

UniProtKB/TrEMBL
        Q75WH8_PSEST | Q75WH8: 2hcv 2i56 2i57 3itl 3ito 3itt 3itv 3itx 3iud 3iuh 3iui 3m0h 3m0l 3m0m 3m0v 3m0x 3m0y 4gji 4gjj

(-) Related Entries Specified in the PDB File

2hcv THE ENZYME (D150N) WITH METAL ION (ZN)
2i56 THE ENZYME (D150N)COMPLEXED WITH L-RHAMNOSE
2i57 THE ENZYME (D150N)COMPLEXED WITH D-ALLOSE
3itl THE ENZYME (D150N, D327N) WITH L-RHAMNULOSE (RING CONFORMATION)
3ito THE ENZYME (D150N, D327N) WITH D-PSICOSE (RING CONFORMATION)
3itt THE ENZYME (D150N, S329K) WITH L-RHAMNOSE (OPEN CONFORMATION)
3itv THE ENZYME (D150N, S329K) WITH D-PSICOSE (OPEN CONFORMATION)
3itx THE ENZYME (D150N) WITH MANGANESE ION
3iud THE ENZYME (D150N) WITH COPPER ION
3iuh THE ENZYME (D150N) WITH COBALT ION
3iui THE ENZYME (D150N) WITH ZINC ION