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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF GLYCOLATE OXIDASE WITH BOUND ACTIVE-SITE INHIBITORS
 
Authors :  K. Stenberg, Y. Lindqvist
Date :  12 Jun 97  (Deposition) - 17 Sep 97  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Flavoprotein, Drug Design, Inhibitor Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Stenberg, Y. Lindqvist
Three-Dimensional Structures Of Glycolate Oxidase With Boun Active-Site Inhibitors.
Protein Sci. V. 6 1009 1997
PubMed-ID: 9144771
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCOLATE OXIDASE
    Cellular Location: PEROXISOME
    Cell Line: BL21
    Chains: A
    EC Number: 1.1.3.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cellular Location: CYTOPLASM
    Expression System Plasmid: PKS20+
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector: PLASMID
    Expression System Vector Type: PLASMID
    Organism Common: SPINACH
    Organism Scientific: SPINACIA OLERACEA
    Organism Taxid: 3562
    Other Details: THE STRUCTURE DESCRIBED IS A COMPLEX OF GLYCOLATE OXIDASE WITH FMN AND AN INHIBITOR

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1DHP1Ligand/Ion3-DECYL-2,5-DIOXO-4-HYDROXY-3-PYRROLINE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1DHP4Ligand/Ion3-DECYL-2,5-DIOXO-4-HYDROXY-3-PYRROLINE
2FMN4Ligand/IonFLAVIN MONONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:25 , ALA A:76 , PRO A:77 , THR A:78 , ALA A:79 , SER A:106 , GLN A:127 , TYR A:129 , THR A:155 , LYS A:230 , SER A:252 , HIS A:254 , GLY A:255 , ARG A:257 , ASP A:285 , GLY A:286 , GLY A:287 , ARG A:289 , GLY A:308 , ARG A:309 , DHP A:361 , HOH A:430 , HOH A:432BINDING SITE FOR RESIDUE FMN A 360
2AC2SOFTWARETYR A:24 , ALA A:79 , TRP A:108 , TYR A:129 , ILE A:168 , PHE A:172 , HIS A:254 , ARG A:257 , FMN A:360BINDING SITE FOR RESIDUE DHP A 361

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1AL8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1AL8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1AL8)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FMN_HYDROXY_ACID_DH_2PS51349 FMN-dependent alpha-hydroxy acid dehydrogenase domain profile.GOX_SPIOL1-359  1A:1-359
2FMN_HYDROXY_ACID_DH_1PS00557 FMN-dependent alpha-hydroxy acid dehydrogenases active site.GOX_SPIOL252-258  1A:252-258
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FMN_HYDROXY_ACID_DH_2PS51349 FMN-dependent alpha-hydroxy acid dehydrogenase domain profile.GOX_SPIOL1-359  4A:1-359
2FMN_HYDROXY_ACID_DH_1PS00557 FMN-dependent alpha-hydroxy acid dehydrogenases active site.GOX_SPIOL252-258  4A:252-258

(-) Exons   (0, 0)

(no "Exon" information available for 1AL8)

(-) 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:344
 aligned with GOX_SPIOL | P05414 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:359
                                    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       340       350         
            GOX_SPIOL     1 MEITNVNEYEAIAKQKLPKMVYDYYASGAEDQWTLAENRNAFSRILFRPRILIDVTNIDMTTTILGFKISMPIMIAPTAMQKMAHPEGEYATARAASAAGTIMTLSSWATSSVEEVASTGPGIRFFQLYVYKDRNVVAQLVRRAERAGFKAIALTVDTPRLGRREADIKNRFVLPPFLTLKNFEGIDLGKMDKANDSGLSSYVAGQIDRSLSWKDVAWLQTITSLPILVKGVITAEDARLAVQHGAAGIIVSNHGARQLDYVPATIMALEEVVKAAQGRIPVFLDGGVRRGTDVFKALALGAAGVFIGRPVVFSLAAEGEAGVKKVLQMMRDEFELTMALSGCRSLKEISRSHIAADWD 359
               SCOP domains d1al8a_ A: Glycolate oxidase                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1al8A00 A:1-359 Aldolase class I                                                                                                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhh.................eee..eee...eee.....hhh....hhhhhhhhhhh....eee.......hhhhhhh....eeeee.....hhhhhhhhhhhhh....eeeee......------.............hhh.....---------......hhh......hhhhhhhhhh...eeeeeee..hhhhhhhhh....eeee.............hhhhhhhhhhhh....eeeee.....hhhhhhhhh....eeee.hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh....hhh..hhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) FMN_HYDROXY_ACID_DH_2  PDB: A:1-359 UniProt: 1-359                                                                                                                                                                                                                                                                                                                      PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FMN_HYD----------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1al8 A   1 MEITNVNEYEAIAKQKLPKMVYDYYASGAEDQWTLAENRNAFSRILFRPRILIDVTNIDMTTTILGFKISMPIMIAPTAMQKMAHPEGEYATARAASAAGTIMTLSSWATSSVEEVASTGPGIRFFQLYVYKDRNVVAQLVRRAERAGFKAIALTVDTPRL------IKNRFVLPPFLTLKNFEGIDL---------GLSSYVAGQIDRSLSWKDVAWLQTITSLPILVKGVITAEDARLAVQHGAAGIIVSNHGARQLDYVPATIMALEEVVKAAQGRIPVFLDGGVRRGTDVFKALALGAAGVFIGRPVVFSLAAEGEAGVKKVLQMMRDEFELTMALSGCRSLKEISRSHIAADWD 359
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160|      170       180       | -       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350         
                                                                                                                                                                                          161    168                 188       198
   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, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1AL8)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (GOX_SPIOL | P05414)
molecular function
    GO:0003973    (S)-2-hydroxy-acid oxidase activity    Catalysis of the reaction: (S)-2-hydroxy-acid + O2 = 2-oxo acid + hydrogen peroxide.
    GO:0010181    FMN binding    Interacting selectively and non-covalently with flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0052853    long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity    Catalysis of the reaction: long-chain-(S)-2-hydroxy-acid + O2 = long-chain-2-oxo acid + hydrogen peroxide. Long chain refers to a chain length of 14 to 18 carbons.
    GO:0052854    medium-chain-(S)-2-hydroxy-acid oxidase activity    Catalysis of the reaction: medium-chain-(S)-2-hydroxy-acid + O2 = medium-chain-2-oxo acid + hydrogen peroxide. Medium chain refers to a chain length of between 8 and 12 carbons.
    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:0052852    very-long-chain-(S)-2-hydroxy-acid oxidase activity    Catalysis of the reaction: very-long-chain (S)-2-hydroxy-acid + O2 = very-long-chain 2-oxo acid + hydrogen peroxide. Very long chain refers to a chain length of greater than 18 carbons.
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.
    GO:0009854    oxidative photosynthetic carbon pathway    The reactions of the C2 pathway bring about the metabolic conversion of two molecules of 2-phosphoglycolate to one molecule of 3-phosphoglycerate, which can be used by the C3 cycle, and one molecule of carbon dioxide (CO2).
    GO:0009853    photorespiration    A light-dependent catabolic process occurring concomitantly with photosynthesis in plants (especially C3 plants) whereby dioxygen (O2) is consumed and carbon dioxide (CO2) is evolved. The substrate is glycolate formed in large quantities in chloroplasts from 2-phosphoglycolate generated from ribulose 1,5-bisphosphate by the action of ribulose-bisphosphate carboxylase; the glycolate enters the peroxisomes where it is converted by glycolate oxidase to glyoxylate which undergoes transamination to glycine. This then passes into the mitochondria where it is decarboxylated forming one molecule of serine for every two molecules of glycine. This pathway also exists in photosynthetic bacteria.
cellular component
    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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        GOX_SPIOL | P05414: 1al7 1gox 1gyl 1huv 1p4c 1p5b 2a7n 2a7p 2a85 3giy

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