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(-) Description

Title :  STRUCTURE OF THERMOPLASMA ACIDOPHILUM ALDOHEXOSE DEHYDROGENASE (ALDT) IN COMPLEX WITH D-MANNOSE
 
Authors :  Y. Yasutake, Y. Nishiya, N. Tamura, T. Tamura
Date :  18 Jul 06  (Deposition) - 27 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yasutake, Y. Nishiya, N. Tamura, T. Tamura
Structural Insights Into Unique Substrate Selectivity Of Thermoplasma Acidophilumd-Aldohexose Dehydrogenase
J. Mol. Biol. V. 367 1034 2007
PubMed-ID: 17300803  |  Reference-DOI: 10.1016/J.JMB.2007.01.029
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUCOSE 1-DEHYDROGENASE RELATED PROTEIN
    Chains: A, B
    EC Number: 1.1.1.118
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TA0754
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303
    Synonym: ALDOHEXOSE DEHYDROGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2SO44Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:84 , SER A:132 , GLN A:134 , TYR A:145 , ALA A:175 , THR A:176 , LEU A:245 , HOH A:633 , HOH A:771 , HOH A:773BINDING SITE FOR RESIDUE BMA A 301
2AC2SOFTWAREMET A:17 , GLY A:18 , ILE A:19 , GLY A:20 , ASN A:80 , HOH A:488 , HOH A:506 , HOH A:778BINDING SITE FOR RESIDUE SO4 A 351
3AC3SOFTWAREGLU B:84 , SER B:132 , GLN B:134 , TYR B:145 , ALA B:175 , THR B:176 , HOH B:551 , HOH B:772 , HOH B:774BINDING SITE FOR RESIDUE BMA B 302
4AC4SOFTWAREMET B:17 , GLY B:18 , ILE B:19 , GLY B:20 , ASN B:80 , LEU B:181 , HOH B:494 , HOH B:624 , HOH B:664BINDING SITE FOR RESIDUE SO4 B 352

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:173 -A:238
2B:173 -B:238

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:164 -Pro A:165
2Ala B:164 -Pro B:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DTX)

(-) 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:255
 aligned with Q9HK51_THEAC | Q9HK51 from UniProtKB/TrEMBL  Length:255

    Alignment length:255
                                    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     
         Q9HK51_THEAC     1 MFSDLRDKVVIVTGASMGIGRAIAERFVDEGSKVIDLSIHDPGEAKYDHIECDVTNPDQVKASIDHIFKEYGSISVLVNNAGIESYGKIESMSMGEWRRIIDVNLFGYYYASKFAIPYMIRSRDPSIVNISSVQASIITKNASAYVTSKHAVIGLTKSIALDYAPLLRCNAVCPATIDTPLVRKAAELEVGSDPMRIEKKISEWGHEHPMQRIGKPQEVASAVAFLASREASFITGTCLYVDGGLSIRAPISTPE 255
               SCOP domains d2dtxa_ A: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.........eeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dtx A   1 GFSDLRDKVVIVTGASMGIGRAIAERFVDEGSKVIDLSIHDPGEAKYDHIECDVTNPDQVKASIDHIFKEYGSISVLVNNAGIESYGKIESMSMGEWRRIIDVNLFGYYYASKFAIPYMIRSRDPSIVNISSVQASIITKNASAYVTSKHAVIGLTKSIALDYAPLLRCNAVCPATIDTPLVRKAAELEVGSDPMRIEKKISEWGHEHPMQRIGKPQEVASAVAFLASREASFITGTCLYVDGGLSIRAPISTPE 255
                                    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     


Chain B from PDB  Type:PROTEIN  Length:255
 aligned with Q9HK51_THEAC | Q9HK51 from UniProtKB/TrEMBL  Length:255

    Alignment length:255
                                    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     
         Q9HK51_THEAC     1 MFSDLRDKVVIVTGASMGIGRAIAERFVDEGSKVIDLSIHDPGEAKYDHIECDVTNPDQVKASIDHIFKEYGSISVLVNNAGIESYGKIESMSMGEWRRIIDVNLFGYYYASKFAIPYMIRSRDPSIVNISSVQASIITKNASAYVTSKHAVIGLTKSIALDYAPLLRCNAVCPATIDTPLVRKAAELEVGSDPMRIEKKISEWGHEHPMQRIGKPQEVASAVAFLASREASFITGTCLYVDGGLSIRAPISTPE 255
               SCOP domains d2dtxb_ B: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..eeeee...hhhhhhhhhhhhhh..eeeeee.........eeee....hhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dtx B   1 GFSDLRDKVVIVTGASMGIGRAIAERFVDEGSKVIDLSIHDPGEAKYDHIECDVTNPDQVKASIDHIFKEYGSISVLVNNAGIESYGKIESMSMGEWRRIIDVNLFGYYYASKFAIPYMIRSRDPSIVNISSVQASIITKNASAYVTSKHAVIGLTKSIALDYAPLLRCNAVCPATIDTPLVRKAAELEVGSDPMRIEKKISEWGHEHPMQRIGKPQEVASAVAFLASREASFITGTCLYVDGGLSIRAPISTPE 255
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2DTX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9HK51_THEAC | Q9HK51)
molecular function
    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.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

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

UniProtKB/TrEMBL
        Q9HK51_THEAC | Q9HK51: 2dtd 2dte 2zk7

(-) Related Entries Specified in the PDB File

2dtd THE SAME PROTEIN IN LIGAND-FREE FORM.
2dte THE SAME PROTEIN IN COMPLEX WITH NADH.