Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF GLYCEROL-3-PHOSPHATE DEHYDROGENASE FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  S. Sakasegawa, C. H. Hagemeier, R. K. Thauer, L. O. Essen, S. Shima
Date :  05 Jul 04  (Deposition) - 07 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Sakasegawa, C. H. Hagemeier, R. K. Thauer, L. O. Essen, S. Shima
Structural And Functional Analysis Of The Gpsa Gene Product Of Archaeoglobus Fulgidus: A Glycerol-3-Phosphate Dehydrogenase With An Unusual Nadp+ Preference
Protein Sci. V. 13 3161 2004
PubMed-ID: 15557260  |  Reference-DOI: 10.1110/PS.04980304

(-) Compounds

Molecule 1 - GLYCEROL-3-PHOSPHATE DEHYDROGENASE [NAD(P)+]
    Chains: A, B
    EC Number: 1.1.1.94
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PEGPD1
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234
    Synonym: NADP, H-DEPENDENT GLYCEROL-3-PHOSPHATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2NH41Ligand/IonAMMONIUM ION
3SO48Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG B:147 , HOH B:1175 , HOH B:1292BINDING SITE FOR RESIDUE SO4 B 1001
02AC2SOFTWARELYS A:53 , ASN A:55 , HOH A:1070 , HOH A:1126BINDING SITE FOR RESIDUE SO4 A 1002
03AC3SOFTWARELYS A:105 , LYS A:192 , ASN A:193 , HOH A:1078 , HOH A:1239BINDING SITE FOR RESIDUE SO4 A 1003
04AC4SOFTWAREARG A:256 , GLY A:257 , GLY A:258 , HOH A:1052 , HOH A:1159BINDING SITE FOR RESIDUE SO4 A 1004
05AC5SOFTWAREARG A:203 , ARG A:256 , GOL A:1009 , HOH A:1067 , HOH A:1158 , HOH A:1334BINDING SITE FOR RESIDUE SO4 A 1005
06AC6SOFTWAREARG B:256 , GLY B:257 , GLY B:258 , HOH B:1065 , HOH B:1197 , HOH B:1201 , HOH B:1243BINDING SITE FOR RESIDUE SO4 B 1006
07AC7SOFTWARELYS B:105 , LYS B:192 , ASN B:193 , HOH B:1120 , HOH B:1145 , HOH B:1280BINDING SITE FOR RESIDUE SO4 B 1007
08AC8SOFTWAREGLY B:258 , ARG B:259 , HOH B:1341BINDING SITE FOR RESIDUE SO4 B 1008
09AC9SOFTWARELEU B:115 , THR B:116 , GLU B:119 , HOH B:1114 , HOH B:1381 , HOH B:1382BINDING SITE FOR RESIDUE NH4 B 1011
10BC1SOFTWAREALA A:200 , ARG A:203 , LYS A:217 , PHE A:255 , SO4 A:1005 , HOH A:1020 , HOH A:1031 , HOH A:1112BINDING SITE FOR RESIDUE GOL A 1009
11BC2SOFTWAREALA B:200 , ARG B:203 , LYS B:217 , PHE B:255 , HOH B:1022 , HOH B:1059 , HOH B:1248BINDING SITE FOR RESIDUE GOL B 1010

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1TXG)

(-) 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:335
 aligned with GPDA_ARCFU | O29390 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:335
                                    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     
           GPDA_ARCFU     1 MIVSILGAGAMGSALSVPLVDNGNEVRIWGTEFDTEILKSISAGREHPRLGVKLNGVEIFWPEQLEKCLENAEVVLLGVSTDGVLPVMSRILPYLKDQYIVLISKGLIDFDNSVLTVPEAVWRLKHDLRERTVAITGPAIAREVAKRMPTTVVFSSPSESSANKMKEIFETEYFGVEVTTDIIGTEITSALKNVYSIAIAWIRGYESRKNVEMSNAKGVIATRAINEMAELIEILGGDRETAFGLSGFGDLIATFRGGRNGMLGELLGKGLSIDEAMEELERRGVGVVEGYKTAEKAYRLSSKINADTKLLDSIYRVLYEGLKVEEVLFELATFK 335
               SCOP domains d1txga2 A:1-180 Glycerol-3- phosphate dehydrogenase                                                                                                                                 d1txga1 A:181-335 Glycerol-3-phosphate dehydrogenase                                                                                                        SCOP domains
               CATH domains 1txgA01 A:1-180 NAD(P)-binding Rossmann-like Domain                                                                                                                                 1txgA02 A:181-335 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhhhh.............eeeehhhhhhhhhh...eeee..hhhhhhhhhhhhh......eeee....eeee..eeeehhhhhhh....hhh.eeeee...hhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1txg A   1 MIVSILGAGAMGSALSVPLVDNGNEVRIWGTEFDTEILKSISAGREHPRLGVKLNGVEIFWPEQLEKCLENAEVVLLGVSTDGVLPVMSRILPYLKDQYIVLISKGLIDFDNSVLTVPEAVWRLKHDLRERTVAITGPAIAREVAKRMPTTVVFSSPSESSANKMKEIFETEYFGVEVTTDIIGTEITSALKNVYSIAIAWIRGYESRKNVEMSNAKGVIATRAINEMAELIEILGGDRETAFGLSGFGDLIATFRGGRNGMLGELLGKGLSIDEAMEELERRGVGVVEGYKTAEKAYRLSSKINADTKLLDSIYRVLYEGLKVEEVLFELATFK 335
                                    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     


Chain B from PDB  Type:PROTEIN  Length:335
 aligned with GPDA_ARCFU | O29390 from UniProtKB/Swiss-Prot  Length:335

    Alignment length:335
                                    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     
           GPDA_ARCFU     1 MIVSILGAGAMGSALSVPLVDNGNEVRIWGTEFDTEILKSISAGREHPRLGVKLNGVEIFWPEQLEKCLENAEVVLLGVSTDGVLPVMSRILPYLKDQYIVLISKGLIDFDNSVLTVPEAVWRLKHDLRERTVAITGPAIAREVAKRMPTTVVFSSPSESSANKMKEIFETEYFGVEVTTDIIGTEITSALKNVYSIAIAWIRGYESRKNVEMSNAKGVIATRAINEMAELIEILGGDRETAFGLSGFGDLIATFRGGRNGMLGELLGKGLSIDEAMEELERRGVGVVEGYKTAEKAYRLSSKINADTKLLDSIYRVLYEGLKVEEVLFELATFK 335
               SCOP domains d1txgb2 B:1-180 Glycerol-3- phosphate dehydrogenase                                                                                                                                 d1txgb1 B:181-335 Glycerol-3-phosphate dehydrogenase                                                                                                        SCOP domains
               CATH domains 1txgB01 B:1-180 NAD(P)-binding Rossmann-like Domain                                                                                                                                 1txgB02 B:181-335 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                                 CATH domains
           Pfam domains (1) -NAD_Gly3P_dh_N-1txgB03 B:2-162                                                                                                                                   -----------------NAD_Gly3P_dh_C-1txgB01 B:180-331                                                                                                                        ---- Pfam domains (1)
           Pfam domains (2) -NAD_Gly3P_dh_N-1txgB04 B:2-162                                                                                                                                   -----------------NAD_Gly3P_dh_C-1txgB02 B:180-331                                                                                                                        ---- Pfam domains (2)
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh..eeeee....hhhhhhhhhh.............eeeehhhhhhhhhh...eeee..hhhhhhhhhhhhh......eeee....eeee..eeeehhhhhhhhhhhhhh.eeeee...hhhhhhh...eeeeee..hhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1txg B   1 MIVSILGAGAMGSALSVPLVDNGNEVRIWGTEFDTEILKSISAGREHPRLGVKLNGVEIFWPEQLEKCLENAEVVLLGVSTDGVLPVMSRILPYLKDQYIVLISKGLIDFDNSVLTVPEAVWRLKHDLRERTVAITGPAIAREVAKRMPTTVVFSSPSESSANKMKEIFETEYFGVEVTTDIIGTEITSALKNVYSIAIAWIRGYESRKNVEMSNAKGVIATRAINEMAELIEILGGDRETAFGLSGFGDLIATFRGGRNGMLGELLGKGLSIDEAMEELERRGVGVVEGYKTAEKAYRLSSKINADTKLLDSIYRVLYEGLKVEEVLFELATFK 335
                                    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
   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  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: 6PGD_C (47)
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GPDA_ARCFU | O29390)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0047952    glycerol-3-phosphate dehydrogenase [NAD(P)+] activity    Catalysis of the reaction: sn-glycerol 3-phosphate + NAD(P)+ = glycerone phosphate + NAD(P)H + H+.
    GO:0004367    glycerol-3-phosphate dehydrogenase [NAD+] activity    Catalysis of the reaction: sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH + H+.
    GO:0036439    glycerol-3-phosphate dehydrogenase [NADP+] activity    Catalysis of the reaction: glycerol 3-phosphate + NADP+ = glycerone phosphate + H+ + NADPH.
    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.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0046167    glycerol-3-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of glycerol-3-phosphate, a phosphoric monoester of glycerol.
    GO:0046168    glycerol-3-phosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of glycerol-3-phosphate, a phosphoric monoester of glycerol.
    GO:0006072    glycerol-3-phosphate metabolic process    The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
    GO:0006650    glycerophospholipid metabolic process    The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0009331    glycerol-3-phosphate dehydrogenase complex    An enzyme complex that catalyzes the dehydrogenation of sn-glycerol 3-phosphate to form glycerone phosphate.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NH4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1txg)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1txg
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  GPDA_ARCFU | O29390
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.1.1.94
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  GPDA_ARCFU | O29390
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1TXG)

(-) Related Entries Specified in the PDB File

1evy CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3- PHOSPHATE DEHYDROGENASE