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(-) Description

Title :  CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA GLYCEROL-3-PHOSPHATE DEHYDROGENASE COMPLEXED WITH DHAP AND NAD
 
Authors :  J. Choe, W. G. J. Hol
Date :  17 Oct 02  (Deposition) - 27 May 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Nad Binding Domain, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Choe, D. Guerra, P. A. M. Michels, W. G. J. Hol
Leishmania Mexicana Glycerol-3-Phosphate Dehydrogenase Showed Conformational Changes Upon Binding A Bi-Substrate Adduct
J. Mol. Biol. V. 320 335 2003
PubMed-ID: 12758080  |  Reference-DOI: 10.1016/S0022-2836(03)00421-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCEROL-3-PHOSPHATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: LEISHMANIA MEXICANA
    Organism Taxid: 5665

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NDE2Ligand/IonADENOSINE 5'-(TRIHYDROGEN DIPHOSPHATE) P'-5'-ESTERWITH 3-(AMINOCARBONYL)-4-(1-HYDROXYL-2-OXO-3-PHOSPHONOOXY-PROPYL)-1-BETA-D-RIBOFURANOSYLPYRIDINIUMINNER SALT

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:23 , GLY A:24 , ALA A:25 , PHE A:26 , HIS A:45 , MET A:46 , PHE A:63 , VAL A:92 , PRO A:94 , PHE A:97 , THR A:124 , LYS A:125 , GLY A:153 , SER A:155 , PHE A:156 , ALA A:157 , LYS A:210 , ASN A:211 , THR A:267 , SER A:273 , ARG A:274 , ASN A:275 , ALA A:297 , VAL A:298 , GLU A:300 , HOH A:428 , HOH A:460 , HOH A:463 , HOH A:466 , HOH A:467 , HOH A:469 , HOH A:471 , HOH A:486 , HOH A:525 , HOH A:535BINDING SITE FOR RESIDUE NDE A 400
2AC2SOFTWARESER B:23 , GLY B:24 , ALA B:25 , PHE B:26 , HIS B:45 , PHE B:63 , VAL B:92 , PRO B:94 , PHE B:97 , THR B:124 , LYS B:125 , GLY B:153 , SER B:155 , PHE B:156 , ALA B:157 , LYS B:210 , ASN B:211 , THR B:267 , SER B:273 , ARG B:274 , ASN B:275 , ALA B:297 , VAL B:298 , GLU B:300 , HOH B:417 , HOH B:468 , HOH B:473 , HOH B:475 , HOH B:479 , HOH B:525 , HOH B:560BINDING SITE FOR RESIDUE NDE B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N1E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N1E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N1E)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NAD_G3PDHPS00957 NAD-dependent glycerol-3-phosphate dehydrogenase signature.GPDA_LEIME207-228
 		  2A:207-228
B:207-228

(-) Exons   (0, 0)

(no "Exon" information available for 1N1E)

(-) 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:349
 aligned with GPDA_LEIME | P90551 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:349
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348         
           GPDA_LEIME     9 KDELLYLNKAVVFGSGAFGTALAMVLSKKCREVCVWHMNEEEVRLVNEKRENVLFLKGVQLASNITFTSDVEKAYNGAEIILFVIPTQFLRGFFEKSGGNLIAYAKEKQVPVLVCTKGIERSTLKFPAEIIGEFLPSPLLSVLAGPSFAIEVATGVFTCVSIASADINVARRLQRIMSTGDRSFVCWATTDTVGCEVASAVKNVLAIGSGVANGLGMGLNARAALIMRGLLEIRDLTAALGGDGSAVFGLAGLGDLQLTCSSELSRNFTVGKKLGKGLPIEEIQRTSKAVAEGVATADPLMRLAKQLKVKMPLCHQIYEIVYKKKNPRDALADLLSCGLQDEGLPPLFK 357
               SCOP domains d1n1ea2 A:9-197 Glycerol-3- phosphate dehydrogenase                                                                                                                                          d1n1ea1 A:198-357 Glycerol-3-phosphate dehydrogenase                                                                                                             SCOP domains
               CATH domains 1n1eA01 A:9-206 NAD(P)-binding Rossmann-like Domain                                                                                                                                                   -1n1eA02 A:208-356 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                          - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee..hhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhh..............eeee.hhhhhhh....eee..hhhhhhhhhhhhhhhhhhhhhhhh..eee...........hhhhhhh...hhh.eeeee...hhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh....hhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NAD_G3PDH             --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n1e A   9 KDELLYLNKAVVFGSGAFGTALAMVLSKKCREVCVWHMNEEEVRLVNEKRENVLFLKGVQLASNITFTSDVEKAYNGAEIILFVIPTQFLRGFFEKSGGNLIAYAKEKQVPVLVCTKGIERSTLKFPAEIIGEFLPSPLLSVLAGPSFAIEVATGVFTCVSIASADINVARRLQRIMSTGDRSFVCWATTDTVGCEVASAVKNVLAIGSGVANGLGMGLNARAALIMRGLLEIRDLTAALGGDGSAVFGLAGLGDLQLTCSSELSRNFTVGKKLGKGLPIEEIQRTSKAVAEGVATADPLMRLAKQLKVKMPLCHQIYEIVYKKKNPRDALADLLSCGLQDEGLPPLFK 357
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348         


Chain B from PDB  Type:PROTEIN  Length:349
 aligned with GPDA_LEIME | P90551 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:349
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348         
           GPDA_LEIME     9 KDELLYLNKAVVFGSGAFGTALAMVLSKKCREVCVWHMNEEEVRLVNEKRENVLFLKGVQLASNITFTSDVEKAYNGAEIILFVIPTQFLRGFFEKSGGNLIAYAKEKQVPVLVCTKGIERSTLKFPAEIIGEFLPSPLLSVLAGPSFAIEVATGVFTCVSIASADINVARRLQRIMSTGDRSFVCWATTDTVGCEVASAVKNVLAIGSGVANGLGMGLNARAALIMRGLLEIRDLTAALGGDGSAVFGLAGLGDLQLTCSSELSRNFTVGKKLGKGLPIEEIQRTSKAVAEGVATADPLMRLAKQLKVKMPLCHQIYEIVYKKKNPRDALADLLSCGLQDEGLPPLFK 357
               SCOP domains d1n1eb2 B:9-197 Glycerol-3- phosphate dehydrogenase                                                                                                                                          d1n1eb1 B:198-357 Glycerol-3-phosphate dehydrogenase                                                                                                             SCOP domains
               CATH domains 1n1eB01 B:9-206 NAD(P)-binding Rossmann-like Domain                                                                                                                                                   -1n1eB02 B:208-356 N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2                                                                          - CATH domains
           Pfam domains (1) --------NAD_Gly3P_dh_N-1n1eB03 B:17-178                                                                                                                                   -------------------NAD_Gly3P_dh_C-1n1eB01 B:198-342                                                                                                                 --------------- Pfam domains (1)
           Pfam domains (2) --------NAD_Gly3P_dh_N-1n1eB04 B:17-178                                                                                                                                   -------------------NAD_Gly3P_dh_C-1n1eB02 B:198-342                                                                                                                 --------------- Pfam domains (2)
         Sec.struct. author ......eeeeeee..hhhhhhhhhhhhh.eeeeeee..hhhhhhhhhhhh..............eeee.hhhhhhh....eee..hhhhhhhhhhhhhhhhhhhhhhhh..eee...........hhhhhhhh..hhh.eeeee...hhhhhhh...eeeeee..hhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhh....hhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhh....ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NAD_G3PDH             --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n1e B   9 KDELLYLNKAVVFGSGAFGTALAMVLSKKCREVCVWHMNEEEVRLVNEKRENVLFLKGVQLASNITFTSDVEKAYNGAEIILFVIPTQFLRGFFEKSGGNLIAYAKEKQVPVLVCTKGIERSTLKFPAEIIGEFLPSPLLSVLAGPSFAIEVATGVFTCVSIASADINVARRLQRIMSTGDRSFVCWATTDTVGCEVASAVKNVLAIGSGVANGLGMGLNARAALIMRGLLEIRDLTAALGGDGSAVFGLAGLGDLQLTCSSELSRNFTVGKKLGKGLPIEEIQRTSKAVAEGVATADPLMRLAKQLKVKMPLCHQIYEIVYKKKNPRDALADLLSCGLQDEGLPPLFK 357
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348
   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  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GPDA_LEIME | P90551)
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:0004367    glycerol-3-phosphate dehydrogenase [NAD+] activity    Catalysis of the reaction: sn-glycerol 3-phosphate + NAD+ = glycerone phosphate + NADH + H+.
    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: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: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.
cellular component
    GO:0009331    glycerol-3-phosphate dehydrogenase complex    An enzyme complex that catalyzes the dehydrogenation of sn-glycerol 3-phosphate to form glycerone phosphate.
    GO:0020015    glycosome    A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GPDA_LEIME | P90551: 1evy 1evz 1jdj 1m66 1m67 1n1g

(-) Related Entries Specified in the PDB File

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