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(-) Description

Title :  GLYCEROL DEHYDRATASE REACTIVASE
 
Authors :  D. -I. Liao, L. Reiss, I. Turner Jr. , G. Dotson
Date :  04 Dec 02  (Deposition) - 14 Jan 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Glycerol Dehydratase, Reactivase, Molecular Chaperone, Actin-Like Atpase Domain, Beta/Beta/Alpha Swiveling Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. -I. Liao, L. Reiss, I. Turner Jr. , G. Dotson
Structure Of Glycerol Dehydratase Reactivase: A New Type Of Molecular Chaperone
Structure V. 11 109 2003
PubMed-ID: 12517345  |  Reference-DOI: 10.1016/S0969-2126(02)00935-8
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCEROL DEHYDRATASE REACTIVASE ALPHA SUBUNIT
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DHAB4
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573
 
Molecule 2 - GLYCEROL DEHYDRATASE REACTIVASE BETA SUBUNIT
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET23A(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ORF2B
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

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

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR C:104 , ASP C:168 , ASP C:185 , HOH C:757 , GLU D:31BINDING SITE FOR RESIDUE CA A 650
2AC2SOFTWARETHR A:104 , ASP A:168 , ASP A:185 , HOH A:656 , GLU B:31BINDING SITE FOR RESIDUE CA C 650

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1B:26 -B:36
2D:26 -D:36

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ala A:294 -Pro A:295
2Ala A:409 -Pro A:410
3Ala C:294 -Pro C:295
4Ala C:409 -Pro C:410

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NBW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NBW)

(-) Exons   (0, 0)

(no "Exon" information available for 1NBW)

(-) 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 Q59474_KLEPN | Q59474 from UniProtKB/TrEMBL  Length:607

    Alignment length:606
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601      
         Q59474_KLEPN     2 PLIAGIDIGNATTEVALASDYPQARAFVASGIVATTGMKGTRDNIAGTLAALEQALAKTPWSMSDVSRIYLNEAAPVIGDVAMETITETIITESTMIGHNPQTPGGVGVGVGTTIALGRLATLPAAQYAEGWIVLIDDAVDFLDAVWWLNEALDRGINVVAAILKKDDGVLVNNRLRKTLPVVDEVTLLEQVPEGVMAAVEVAAPGQVVRILSNPYGIATFFGLSPEETQAIVPIARALIGNRSAVVLKTPQGDVQSRVIPAGNLYISGEKRRGEADVAEGAEAIMQAMSACAPVRDIRGEPGTHAGGMLERVRKVMASLTGHEMSAIYIQDLLAVDTFIPRKVQGGMAGECAMENAVGMAAMVKADRLQMQVIARELSARLQTEVVVGGVEANMAIAGALTTPGCAAPLAILDLGAGSTDAAIVNAEGQITAVHLAGAGNMVSLLIKTELGLEDLSLAEAIKKYPLAKVESLFSIRHENGAVEFFREALSPAVFAKVVYIKEGELVPIDNASPLEKIRLVRRQAKEKVFVTNCLRALRQVSPGGSIRDIAFVVLVGGSSLDFEIPQLITEALSHYGVVAGQGNIRGTEGPRNAVATGLLLAGQAN 607
               SCOP domains d1nbwa2 A:2-91,A:257-405                                                                  d1nbwa1 A:92-256 Swiveling domain of the glycerol dehydratase reactivase alpha subunit                                                                               d1nbwa2 A:2-91,A:257-405 ATPase domain of the glycerol dehydratase reactivase alpha subunit                                                          d1nbwa3 A:406-607 ATPase domain of the glycerol dehydratase reactivase alpha subunit                                                                                                                       SCOP domains
               CATH domains 1nbwA01 A:2-75,A:373-406,A:584-607  [code=3.30.420.40, no name defined]   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1nbwA01 A:2-75,A:373-406,A:584-607---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1nbwA01                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee...eeeeeeee.........eeeeee......hhhhhhhhhhhhhhhhh....hhh.eeeeeeee...eeeeeeeee.eeeeee...ee..........eeeeeeeee.hhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhh...eeeeee...hhhhhhh.......ee....hhhhh....eeeeee...........hhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeee.....eeeeee....eeeeee...eeeee...hhhhhhhhhhhhh.eeeeee...hhhhhhhhhhhhhhhhhh..hhhhh...eeeeeeeeeeee........eeeeeeeeeeeeee.......hhhhhhhhhhh.eeee..hhhhhhhhhhh........eeeeee...eeeeeee.....eeeeeee.hhhhhhhhhhhhhh..hhhhhhhhhhh.eeee....eeee....eee.....hhhhh..eeeee..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh............eeeeehhhhhh.hhhhhhhhhhhh...eeee.hhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1nbw A   2 PLIAGIDIGNATTEVALASDYPQARAFVASGIVATTGMKGTRDNIAGTLAALEQALAKTPWSMSDVSRIYLNEAAPVIGDVAMETITETIITESTMIGHNPQTPGGVGVGVGTTIALGRLATLPAAQYAEGWIVLIDDAVDFLDAVWWLNEALDRGINVVAAILKKDDGVLVNNRLRKTLPVVDEVTLLEQVPEGVMAAVEVAAPGQVVRILSNPYGIATFFGLSPEETQAIVPIARALIGNRSAVVLKTPQGDVQSRVIPAGNLYISGEKRRGEADVAEGAEAIMQAMSACAPVRDIRGEPGTHAGGMLERVRKVMASLTGHEMSAIYIQDLLAVDTFIPRKVQGGMAGECAMENAVGMAAMVKADRLQMQVIARELSARLQTEVVVGGVEANMAIAGALTTPGCAAPLAILDLGAGSTDAAIVNAEGQITAVHLAGAGNMVSLLIKTELGLEDLSLAEAIKKYPLAKVESLFSIRHENGAVEFFREALSPAVFAKVVYIKEGELVPIDNASPLEKIRLVRRQAKEKVFVTNCLRALRQVSPGGSIRDIAFVVLVGGSSLDFEIPQLITEALSHYGVVAGQGNIRGTEGPRNAVATGLLLAGQAN 607
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601      


Chain B from PDB  Type:PROTEIN  Length:113
 aligned with Q48423_KLEPN | Q48423 from UniProtKB/TrEMBL  Length:117

    Alignment length:113
                                    14        24        34        44        54        64        74        84        94       104       114   
         Q48423_KLEPN     5 PPGVRLFYDPRGHHAGAINELCWGLEEQGVPCQTITYDGGGDAAALGALAARSSPLRVGIGLSASGEIALTHAQLPADAPLATGHVTDSDDQLRTLGANAGQLVKVLPLSERN 117
               SCOP domains d1nbwb_ B: Glycerol dehydratase reactivase, beta subunit                                                          SCOP domains
               CATH domains 1nbwB00 B:5-117 Diol Dehydratase; Chain B                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh...eeeee....eeeeee.........eeee...hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1nbw B   5 PPGVRLFYDPRGHHAGAINELCWGLEEQGVPCQTITYDGGGDAAALGALAARSSPLRVGIGLSASGEIALTHAQLPADAPLATGHVTDSDDQLRTLGANAGQLVKVLPLSERN 117
                                    14        24        34        44        54        64        74        84        94       104       114   


Chain C from PDB  Type:PROTEIN  Length:604
 aligned with Q59474_KLEPN | Q59474 from UniProtKB/TrEMBL  Length:607

    Alignment length:604
                                    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       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602    
         Q59474_KLEPN     3 LIAGIDIGNATTEVALASDYPQARAFVASGIVATTGMKGTRDNIAGTLAALEQALAKTPWSMSDVSRIYLNEAAPVIGDVAMETITETIITESTMIGHNPQTPGGVGVGVGTTIALGRLATLPAAQYAEGWIVLIDDAVDFLDAVWWLNEALDRGINVVAAILKKDDGVLVNNRLRKTLPVVDEVTLLEQVPEGVMAAVEVAAPGQVVRILSNPYGIATFFGLSPEETQAIVPIARALIGNRSAVVLKTPQGDVQSRVIPAGNLYISGEKRRGEADVAEGAEAIMQAMSACAPVRDIRGEPGTHAGGMLERVRKVMASLTGHEMSAIYIQDLLAVDTFIPRKVQGGMAGECAMENAVGMAAMVKADRLQMQVIARELSARLQTEVVVGGVEANMAIAGALTTPGCAAPLAILDLGAGSTDAAIVNAEGQITAVHLAGAGNMVSLLIKTELGLEDLSLAEAIKKYPLAKVESLFSIRHENGAVEFFREALSPAVFAKVVYIKEGELVPIDNASPLEKIRLVRRQAKEKVFVTNCLRALRQVSPGGSIRDIAFVVLVGGSSLDFEIPQLITEALSHYGVVAGQGNIRGTEGPRNAVATGLLLAGQA 606
               SCOP domains d1nbwc2 C:3-91,C:257-405                                                                 d1nbwc1 C:92-256 Swiveling domain of the glycerol dehydratase reactivase alpha subunit                                                                               d1nbwc2 C:3-91,C:257-405 ATPase domain of the glycerol dehydratase reactivase alpha subunit                                                          d1nbwc3 C:406-606 ATPase domain of the glycerol dehydratase reactivase alpha subunit                                                                                                                      SCOP domains
               CATH domains 1nbwC01 C:3-75,C:373-406,C:584-606  [code=3.30.420.40, no name defined]  ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1nbwC01 C:3-75,C:373-406,C:584-606---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1nbwC01                 CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDR-1nbwC01 C:276-606                                                                                                                                                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DDR-1nbwC02 C:276-606                                                                                                                                                                                                                                                                                                                       Pfam domains (2)
         Sec.struct. author .eeeeee...eeeeeee..........eeeeee......hhhhhhhhhhhhhhhhhh...hhhhh.eeeeee...eeeeeeeee.eeeeee...ee..........eeeeeeeee.hhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh..eeeeee...hhhhhhh.......ee....hhhhh....eeeeee...........hhhhhhhhhh.hhhhhhhhhhhhhhhh...eeeee.....eeeeee....eeeeee...eeeee...hhhhhhhhhhhh..eeeeee...hhhhhhhhhhhhhhhhhh..........eeeeeeeeeeee........eeeeeeeeeeeeee.......hhhhhhhhhhh.eeee..hhhhhhhhhhh........eeeeee...eeeeeee.....eeeeeee.hhhhhhhhhhhhhh..hhhhhhhhhhh.eeee....eeee....eee.....hhhhh..eeee....eee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.eeeeehhhhhh.hhhhhhhhhhhh...eeee.hhhhh....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nbw C   3 LIAGIDIGNATTEVALASDYPQARAFVASGIVATTGMKGTRDNIAGTLAALEQALAKTPWSMSDVSRIYLNEAAPVIGDVAMETITETIITESTMIGHNPQTPGGVGVGVGTTIALGRLATLPAAQYAEGWIVLIDDAVDFLDAVWWLNEALDRGINVVAAILKKDDGVLVNNRLRKTLPVVDEVTLLEQVPEGVMAAVEVAAPGQVVRILSNPYGIATFFGLSPEETQAIVPIARALIGNRSAVVLKTPQGDVQSRVIPAGNLYISGEKRRGEADVAEGAEAIMQAMSACAPVRDIRGEPGTHAGGMLERVRKVMASLTGHEMSAIYIQDLLAVDTFIPRKVQGGMAGECAMENAVGMAAMVKADRLQMQVIARELSARLQTEVVVGGVEANMAIAGALTTPGCAAPLAILDLGAGSTDAAIVNAEGQITAVHLAGAGNMVSLLIKTELGLEDLSLAEAIKKYPLAKVESLFSIRHENGAVEFFREALSPAVFAKVVYIKEGELVPIDNASPLEKIRLVRRQAKEKVFVTNCLRALRQVSPGGSIRDIAFVVLVGGSSLDFEIPQLITEALSHYGVVAGQGNIRGTEGPRNAVATGLLLAGQA 606
                                    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       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602    


Chain D from PDB  Type:PROTEIN  Length:113
 aligned with Q48423_KLEPN | Q48423 from UniProtKB/TrEMBL  Length:117

    Alignment length:113
                                    14        24        34        44        54        64        74        84        94       104       114   
         Q48423_KLEPN     5 PPGVRLFYDPRGHHAGAINELCWGLEEQGVPCQTITYDGGGDAAALGALAARSSPLRVGIGLSASGEIALTHAQLPADAPLATGHVTDSDDQLRTLGANAGQLVKVLPLSERN 117
               SCOP domains d1nbwd_ D: Glycerol dehydratase reactivase, beta subunit                                                          SCOP domains
               CATH domains 1nbwD00 D:5-117 Diol Dehydratase; Chain B                                                                         CATH domains
           Pfam domains (1) Dehydratase_MU-1nbwD01 D:5-114                                                                                --- Pfam domains (1)
           Pfam domains (2) Dehydratase_MU-1nbwD02 D:5-114                                                                                --- Pfam domains (2)
         Sec.struct. author ...eeeee.....hhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhh...eeeee....eeeeee.........eeee...hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1nbw D   5 PPGVRLFYDPRGHHAGAINELCWGLEEQGVPCQTITYDGGGDAAALGALAARSSPLRVGIGLSASGEIALTHAQLPADAPLATGHVTDSDDQLRTLGANAGQLVKVLPLSERN 117
                                    14        24        34        44        54        64        74        84        94       104       114
   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  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Actin_ATPase (173)
(-)
Family: DDR (1)
(-)
Klebsiella pneumoniae (1)
1aDDR-1nbwC01C:276-606
1bDDR-1nbwC02C:276-606
(-)
Clan: no clan defined [family: Dehydratase_MU] (3)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C   (Q59474_KLEPN | Q59474)
molecular function
    GO:0046405    glycerol dehydratase activity    Catalysis of the reaction: glycerol = 3-hydroxypropanal + H2O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

Chain B,D   (Q48423_KLEPN | Q48423)

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