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(-) Description

Title :  STRCUTURE OF DIOL DEHYDRATASE-REACTIVATING FACTOR IN NUCLEOTIDE FREE FORM
 
Authors :  N. Shibata, K. Mori, N. Hieda, Y. Higuchi, M. Yamanishi, T. Toraya
Date :  05 Aug 05  (Deposition) - 28 Feb 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Shibata, K. Mori, N. Hieda, Y. Higuchi, M. Yamanishi, T. Toraya
Release Of A Damaged Cofactor From A Coenzyme B12-Dependent Enzyme: X-Ray Structures Of Diol Dehydratase-Reactivating Factor
Structure V. 13 1745 2005
PubMed-ID: 16338403  |  Reference-DOI: 10.1016/J.STR.2005.08.011
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DIOL DEHYDRATASE-REACTIVATING FACTOR LARGE SUBUNIT
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUSI2E
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: KLEBSIELLA OXYTOCA
    Organism Taxid: 571
 
Molecule 2 - DIOL DEHYDRATASE-REACTIVATING FACTOR SMALL SUBUNIT
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUSI2E
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: KLEBSIELLA OXYTOCA
    Organism Taxid: 571

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric/Biological Unit (2, 7)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2SO45Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , ASN A:11 , SER A:12 , SER A:13 , ASP A:413BINDING SITE FOR RESIDUE SO4 A 611
2AC2SOFTWAREASN A:11 , GLY A:415 , ALA A:416 , GLY A:417 , SER A:418BINDING SITE FOR RESIDUE SO4 A 612
3AC3SOFTWAREARG A:518 , ARG A:522BINDING SITE FOR RESIDUE SO4 A 613
4AC4SOFTWAREARG C:518 , ARG C:522BINDING SITE FOR RESIDUE SO4 C 611
5AC5SOFTWAREASN C:11 , ASP C:413 , GLY C:415 , ALA C:416 , GLY C:417 , SER C:418BINDING SITE FOR RESIDUE SO4 C 612
6AC6SOFTWARETHR A:105 , ASP A:166 , ASP A:183 , GLU A:184 , GLU B:31BINDING SITE FOR RESIDUE CA A 1005
7AC7SOFTWARETHR C:105 , ASP C:166 , ASP C:183 , GLU C:184 , GLU D:31BINDING SITE FOR RESIDUE CA C 1006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D0P)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Arg A:407 -Pro A:408
2Gly C:292 -Arg C:293
3Arg C:407 -Pro C:408

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D0P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2D0P)

(-) Exons   (0, 0)

(no "Exon" information available for 2D0P)

(-) 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:606
 aligned with DDRFA_KLEOK | O68195 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:606
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600      
          DDRFA_KLEOK     1 MRYIAGIDIGNSSTEVALATLDEAGALTITHSALAETTGIKGTLRNVFGIQEALALVARGAGIAVSDISLIRINEATPVIGDVAMETITETIITESTMIGHNPKTPGGAGLGTGITITPQELLTRPADAPYILVVSSAFDFADIASVINASLRAGYQITGVILQRDDGVLVSNRLEKPLPIVDEVLYIDRIPLGMLAAIEVAVPGKVIETLSNPYGIATVFNLSPEETKNIVPMARALIGNRSAVVVKTPSGDVKARAIPAGNLELLAQGRSVRVDVAAGAEAIMKAVDGCGRLDNVTGESGTNIGGMLEHVRQTMAELTNKPSSEIFIQDLLAVDTSVPVSVTGGLAGEFSLEQAVGIASMVKSDRLQMAMIAREIEQKLNIDVQIGGAEAEAAILGALTTPGTTRPLAILDLGAGSTDASIINPKGDIIATHLAGAGDMVTMIIARELGLEDRYLAEEIKKYPLAKVESLFHLRHEDGSVQFFSTPLPPAVFARVCVVKADELVPLPGDLALEKVRAIRRSAKERVFVTNALRALRQVSPTGNIRDIPFVVLVGGSSLDFEVPQLVTDALAHYRLVAGRGNIRGSEGPRNAVATGLILSWHKEF 606
               SCOP domains d2d0pa2 A:1-92,A:255-403 Diol dehydratase-reactivating factor large subunit DdrA            d2d0pa1 A:93-254 Diol dehydratase-reactivating factor large subunit DdrA                                                                                          d2d0pa2 A:1-92,A:255-403 Diol dehydratase-reactivating factor large subunit DdrA                                                                     d2d0pa3 A:404-606 Diol dehydratase-reactivating factor large subunit DdrA                                                                                                                                   SCOP domains
               CATH domains 2d0pA01 A:1-76,A:371-404,A:582-606  [code=3.30.420.40, no name defined]     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2d0pA01 A:1-76,A:371-404,A:582-606---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2d0pA01                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeee...eeeeeeeee.....eeeeeeeeee........hhhhhhhhhhhhhhhhh..hhh.eeeeee.....eeeeee....eeeeee...ee..........eeeeeeee..hhhhhh.....eee......hhhhhhhhhhhhhhhh..eeeee....hhhhhhh.......ee....hhhhh....eeeeee...........hhhhhhhhhh....hhhhhhhhhhhhh...eeeeee....eeeeee....eeeeee..eeeeee...hhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhh....hhhhh...eeeeeeeeeeee........eeeeeeeeeeeeee....hhhhhhhhhhhhhh.eeee..hhhhhhhhhhh........eeeeee...eeeeeee.....eeeeeee.hhhhhhhhhhhhh...hhhhhhhhhhh.eee.....eee.....eee............eeee....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeehhhhhh.hhhhhhhhhhh.........hhhhh....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2d0p A   1 MRYIAGIDIGNSSTEVALATLDEAGALTITHSALAETTGIKGTLRNVFGIQEALALVARGAGIAVSDISLIRINEATPVIGDVAMETITETIITESTMIGHNPKTPGGAGLGTGITITPQELLTRPADAPYILVVSSAFDFADIASVINASLRAGYQITGVILQRDDGVLVSNRLEKPLPIVDEVLYIDRIPLGMLAAIEVAVPGKVIETLSNPYGIATVFNLSPEETKNIVPMARALIGNRSAVVVKTPSGDVKARAIPAGNLELLAQGRSVRVDVAAGAEAIMKAVDGCGRLDNVTGESGTNIGGMLEHVRQTMAELTNKPSSEIFIQDLLAVDTSVPVSVTGGLAGEFSLEQAVGIASMVKSDRLQMAMIAREIEQKLNIDVQIGGAEAEAAILGALTTPGTTRPLAILDLGAGSTDASIINPKGDIIATHLAGAGDMVTMIIARELGLEDRYLAEEIKKYPLAKVESLFHLRHEDGSVQFFSTPLPPAVFARVCVVKADELVPLPGDLALEKVRAIRRSAKERVFVTNALRALRQVSPTGNIRDIPFVVLVGGSSLDFEVPQLVTDALAHYRLVAGRGNIRGSEGPRNAVATGLILSWHKEF 606
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600      


Chain B from PDB  Type:PROTEIN  Length:110
 aligned with O68196_KLEOX | O68196 from UniProtKB/TrEMBL  Length:125

    Alignment length:110
                                    13        23        33        43        53        63        73        83        93       103       113
         O68196_KLEOX     4 NHSAPAIAIAVIDGCDGLWREVLLGIEEEGIPFRLQHHPAGEVVDSAWQAARSSPLLVGIACDRHMLVVHYKNLPASAPLFTLMHHQDSQAHRNTGNNAARLVKGIPFRD 113
               SCOP domains d2d0pb_ B: automated matches                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee.hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh...eeeee...eeeeee.........eeee...hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                 2d0p B   4 NHSAPAIAIAVIDGCDGLWREVLLGIEEEGIPFRLQHHPAGEVVDSAWQAARSSPLLVGIACDRHMLVVHYKNLPASAPLFTLMHHQDSQAHRNTGNNAARLVKGIPFRD 113
                                    13        23        33        43        53        63        73        83        93       103       113


Chain C from PDB  Type:PROTEIN  Length:605
 aligned with DDRFA_KLEOK | O68195 from UniProtKB/Swiss-Prot  Length:610

    Alignment length:605
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600     
          DDRFA_KLEOK     1 MRYIAGIDIGNSSTEVALATLDEAGALTITHSALAETTGIKGTLRNVFGIQEALALVARGAGIAVSDISLIRINEATPVIGDVAMETITETIITESTMIGHNPKTPGGAGLGTGITITPQELLTRPADAPYILVVSSAFDFADIASVINASLRAGYQITGVILQRDDGVLVSNRLEKPLPIVDEVLYIDRIPLGMLAAIEVAVPGKVIETLSNPYGIATVFNLSPEETKNIVPMARALIGNRSAVVVKTPSGDVKARAIPAGNLELLAQGRSVRVDVAAGAEAIMKAVDGCGRLDNVTGESGTNIGGMLEHVRQTMAELTNKPSSEIFIQDLLAVDTSVPVSVTGGLAGEFSLEQAVGIASMVKSDRLQMAMIAREIEQKLNIDVQIGGAEAEAAILGALTTPGTTRPLAILDLGAGSTDASIINPKGDIIATHLAGAGDMVTMIIARELGLEDRYLAEEIKKYPLAKVESLFHLRHEDGSVQFFSTPLPPAVFARVCVVKADELVPLPGDLALEKVRAIRRSAKERVFVTNALRALRQVSPTGNIRDIPFVVLVGGSSLDFEVPQLVTDALAHYRLVAGRGNIRGSEGPRNAVATGLILSWHKE 605
               SCOP domains d2d0pc2 C:1-92,C:255-403 Diol dehydratase-reactivating factor large subunit DdrA            d2d0pc1 C:93-254 Diol dehydratase-reactivating factor large subunit DdrA                                                                                          d2d0pc2 C:1-92,C:255-403 Diol dehydratase-reactivating factor large subunit DdrA                                                                     d2d0pc3 C:404-605 Diol dehydratase-reactivating factor large subunit DdrA                                                                                                                                  SCOP domains
               CATH domains 2d0pC01 C:1-76,C:371-404,C:582-605  [code=3.30.420.40, no name defined]     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2d0pC01 C:1-76,C:371-404,C:582-605---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2d0pC01                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee...eeeeeeeee.....eeeeeeeeee........hhhhhhhhhhhhhhhhh..hhh.eeeeee.....eeeeeeeee.eeeeee...ee..........eeeeeeee..hhhhhh.....eeee.....hhhhhhhhhhhhhhhh..eeeee....hhhhhhh.......ee.............eeeeee...........hhhhhhhhhh....hhhhhhhhhhhhh...eeeee.....eeeeee....eeeeee..eeeeee...hhhhhhhhhhh.....eee....hhhhhhhhhhh.................eeeeeeeeeeee........eeeeeeeeeeeeee....hhhhhhhhhhhhhh.eeee..hhhhhhhhhhh........eeeeee...eeeeeee.....eeeeeee.hhhhhhhhhhhhh...hhhhhhhhhhh.eeeeee..eee.....eee............eeee....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.eeeeehhhhhh.hhhhhhhhhhh.........hhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d0p C   1 MRYIAGIDIGNSSTEVALATLDEAGALTITHSALAETTGIKGTLRNVFGIQEALALVARGAGIAVSDISLIRINEATPVIGDVAMETITETIITESTMIGHNPKTPGGAGLGTGITITPQELLTRPADAPYILVVSSAFDFADIASVINASLRAGYQITGVILQRDDGVLVSNRLEKPLPIVDEVLYIDRIPLGMLAAIEVAVPGKVIETLSNPYGIATVFNLSPEETKNIVPMARALIGNRSAVVVKTPSGDVKARAIPAGNLELLAQGRSVRVDVAAGAEAIMKAVDGCGRLDNVTGESGTNIGGMLEHVRQTMAELTNKPSSEIFIQDLLAVDTSVPVSVTGGLAGEFSLEQAVGIASMVKSDRLQMAMIAREIEQKLNIDVQIGGAEAEAAILGALTTPGTTRPLAILDLGAGSTDASIINPKGDIIATHLAGAGDMVTMIIARELGLEDRYLAEEIKKYPLAKVESLFHLRHEDGSVQFFSTPLPPAVFARVCVVKADELVPLPGDLALEKVRAIRRSAKERVFVTNALRALRQVSPTGNIRDIPFVVLVGGSSLDFEVPQLVTDALAHYRLVAGRGNIRGSEGPRNAVATGLILSWHKE 605
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600     


Chain D from PDB  Type:PROTEIN  Length:109
 aligned with O68196_KLEOX | O68196 from UniProtKB/TrEMBL  Length:125

    Alignment length:109
                                    14        24        34        44        54        64        74        84        94       104         
         O68196_KLEOX     5 HSAPAIAIAVIDGCDGLWREVLLGIEEEGIPFRLQHHPAGEVVDSAWQAARSSPLLVGIACDRHMLVVHYKNLPASAPLFTLMHHQDSQAHRNTGNNAARLVKGIPFRD 113
               SCOP domains d2d0pd_ D: automated matches                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.hhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhh...eeeee...eeeeee.........eeee...hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 2d0p D   5 HSAPAIAIAVIDGCDGLWREVLLGIEEEGIPFRLQHHPAGEVVDSAWQAARSSPLLVGIACDRHMLVVHYKNLPASAPLFTLMHHQDSQAHRNTGNNAARLVKGIPFRD 113
                                    14        24        34        44        54        64        74        84        94       104
   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  (3, 8)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D0P)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (DDRFA_KLEOK | O68195)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.

Chain B,D   (O68196_KLEOX | O68196)

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  2d0p
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 Related Entries

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

UniProtKB/Swiss-Prot
        DDRFA_KLEOK | O68195: 2d0o
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        O68196_KLEOX | O68196: 2d0o

(-) Related Entries Specified in the PDB File

2d0o COMPLEXED WITH ADP AND MG2+