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(-) Description

Title :  CRYSTAL STRUCTURE OF A GLYCEROL DEHYDROGENASE (TM0423) FROM THERMOTOGA MARITIMA AT 1.5 A RESOLUTION
 
Authors :  I. A. Wilson, M. D. Miller, Joint Center For Structural Genomics (
Date :  03 Jan 02  (Deposition) - 27 Feb 02  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (8x)
Keywords :  Glycerol Dehydrogenase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Lesley, P. Kuhn, A. Godzik, A. M. Deacon, I. Mathews, A. Kreusch, G. Spraggon, H. E. Klock, D. Mcmullan, T. Shin, J. Vincent, A. Robb, L. S. Brinen, M. D. Miller, T. M. Mcphillips, M. A. Miller, D. Scheibe, J. M. Canaves, C. Guda, L. Jaroszewski, T. L. Selby, M. -A. Elsliger, J. Wooley, S. S. Taylor, K. O. Hodgson, I. A. Wilson, P. G. Schultz, R. C. Stevens
Structural Genomics Of The Thermotoga Maritima Proteome Implemented In A High-Throughput Structure Determination Pipeline
Proc. Natl. Acad. Sci. Usa V. 99 11664 2002
PubMed-ID: 12193646  |  Reference-DOI: 10.1073/PNAS.142413399

(-) Compounds

Molecule 1 - GLYCEROL DEHYDROGENASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMH1
    Expression System Strain: DL41
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TM0423
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (8x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2TRS8Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:169 , HIS A:252 , HIS A:269 , TRS A:2922BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWAREASP A:119 , ASP A:169 , THR A:173 , SER A:239 , HIS A:252 , TRS A:2922 , HOH A:2932BINDING SITE FOR RESIDUE CL A 501
3AC3SOFTWAREASP A:119 , ASP A:169 , PHE A:243 , HIS A:252 , HIS A:269 , ZN A:401 , CL A:501 , HOH A:3121BINDING SITE FOR RESIDUE TRS A 2922

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KQ3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1KQ3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KQ3)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_IRON_1PS00913 Iron-containing alcohol dehydrogenases signature 1.GLDA_THEMA148-176  1A:148-176
2ADH_IRON_2PS00060 Iron-containing alcohol dehydrogenases signature 2.GLDA_THEMA239-259  1A:239-259
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_IRON_1PS00913 Iron-containing alcohol dehydrogenases signature 1.GLDA_THEMA148-176  1A:148-176
2ADH_IRON_2PS00060 Iron-containing alcohol dehydrogenases signature 2.GLDA_THEMA239-259  1A:239-259
Biological Unit 2 (2, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADH_IRON_1PS00913 Iron-containing alcohol dehydrogenases signature 1.GLDA_THEMA148-176  8A:148-176
2ADH_IRON_2PS00060 Iron-containing alcohol dehydrogenases signature 2.GLDA_THEMA239-259  8A:239-259

(-) Exons   (0, 0)

(no "Exon" information available for 1KQ3)

(-) 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:364
 aligned with GLDA_THEMA | Q9WYQ4 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:364
                             1                                                                                                                                                                                                                                                                                                                                                                          
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359    
           GLDA_THEMA     - -MITTTIFPGRYVQGAGAINILEEELSRFGERAFVVIDDFVDKNVLGENFFSSFTKVRVNKQIFGGECSDEEIERLSGLVEEETDVVVGIGGGKTLDTAKAVAYKLKKPVVIVPTIASTDAPCSALSVIYTPNGEFKRYLFLPRNPDVVLVDTEIVAKAPARFLVAGMGDALATWFEAESCKQKYAPNMTGRLGSMTAYALARLCYETLLEYGVLAKRSVEEKSVTPALEKIVEANTLLSGLGFESGGLAAAHAIHNGLTVLENTHKYLHGEKVAIGVLASLFLTDKPRKMIEEVYSFCEEVGLPTTLAEIGLDGVSDEDLMKVAEKACDKNETIHNEPQPVTSKDVFFALKAADRYGRMRKNL 363
               SCOP domains d1kq3a_ A: Glycerol dehydrogenase                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1kq3A01 A:0-157  [code=3.40.50.1970, no name defined]                                                                                                         1kq3A02 A:158-363 Dehydroquinate synthase-like - alpha domain                                                                                                                                                  CATH domains
               Pfam domains --------Fe-ADH-1kq3A01 A:8-346                                                                                                                                                                                                                                                                                                                             ----------------- Pfam domains
         Sec.struct. author ..........eeeee.hhhhhhhhhhhh...eeeeeehhhhhhhh...hhhhhh...eeeeee.....hhhhhhhhhh.......eeeeeehhhhhhhhhhhhhhh...eeeee...........eeeee.....eeeeee......eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------ADH_IRON_1  PDB: A:148-176   --------------------------------------------------------------ADH_IRON_2           -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kq3 A   0 HMITTTIFPGRYVQGAGAINILEEELSRFGERAFVVIDDFVDKNVLGENFFSSFTKVRVNKQIFGGECSDEEIERLSGLVEEETDVVVGIGGGKTLDTAKAVAYKLKKPVVIVPTIASTDAPCSALSVIYTPNGEFKRYLFLPRNPDVVLVDTEIVAKAPARFLVAGMGDALATWFEAESCKQKYAPNMTGRLGSMTAYALARLCYETLLEYGVLAKRSVEEKSVTPALEKIVEANTLLSGLGFESGGLAAAHAIHNGLTVLENTHKYLHGEKVAIGVLASLFLTDKPRKMIEEVYSFCEEVGLPTTLAEIGLDGVSDEDLMKVAEKACDKNETIHNEPQPVTSKDVFFALKAADRYGRMRKNL 363
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
   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  (1, 1)

Asymmetric Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: DHQS (27)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (GLDA_THEMA | Q9WYQ4)
molecular function
    GO:0008888    glycerol dehydrogenase [NAD+] activity    Catalysis of the reaction: glycerol + NAD(+) = glycerone + H(+) + NADH.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0019588    anaerobic glycerol catabolic process    The anaerobic chemical reactions and pathways resulting in the breakdown of glycerol, yielding energy in the form of ATP.
    GO:0006071    glycerol metabolic process    The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    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

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(-) Related Entries Specified in the PDB File

1jpu CRYSTAL STRUCTURE OF BACILLUS STEAROTHERMOPHILUS GLYCEROL DEHYDROGENASE
1jq5 BACILLUS STEAROTHERMOPHILUS GLYCEROL DEHYDROGENASE COMPLEX WITH NAD+
1jqa BACILLUS STERATHERMOPHILUS GLYCEROL DEHYDROGENASE COMPLEX WITH GLYCEROL RELATED ID: 282296 RELATED DB: TARGETDB