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(-) Description

Title :  STRUCTURE OF THIO (GLYCINE OXIDASE) FROM BACILLUS SUBTILIS
 
Authors :  E. C. Settembre, P. C. Dorrestein, J. Park, A. Augustine, T. P. Begley, S
Date :  16 Dec 02  (Deposition) - 08 Apr 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Flavoprotein, Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. C. Settembre, P. C. Dorrestein, J. Park, A. Augustine, T. P. Begley, S. E. Ealick
Structural And Mechanistic Studies On Thio, A Glycine Oxidase Essential For Thiamin Biosynthesis In Bacillus Subtilis
Biochemistry V. 42 2971 2003
PubMed-ID: 12627963  |  Reference-DOI: 10.1021/BI026916V

(-) Compounds

Molecule 1 - GLYCINE OXIDASE
    ChainsA, B
    EC Number1.5.3.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET16-B
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneGOXB
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PEO2Ligand/IonHYDROGEN PEROXIDE
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PEO4Ligand/IonHYDROGEN PEROXIDE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:89 , ARG A:254 , ARG B:89 , ARG B:254BINDING SITE FOR RESIDUE PO4 B 402
2AC2SOFTWAREGLY A:11 , GLY A:13 , ILE A:14 , ILE A:15 , PHE A:33 , GLU A:34 , SER A:35 , ARG A:41 , THR A:42 , THR A:43 , ALA A:46 , ALA A:47 , GLY A:48 , MET A:49 , VAL A:174 , SER A:202 , GLY A:203 , TRP A:205 , PHE A:209 , CYS A:226 , TYR A:246 , GLY A:300 , ARG A:302 , HIS A:327 , ARG A:329 , ASN A:330 , GLY A:331 , ILE A:332 , LEU A:333 , PEO A:401 , HOH A:402 , HOH A:403 , HOH A:404 , HOH A:408 , HOH A:412 , HOH A:421BINDING SITE FOR RESIDUE FAD A 400
3AC3SOFTWAREARG A:302 , ARG A:329 , FAD A:400 , HOH A:436 , HOH A:484BINDING SITE FOR RESIDUE PEO A 401
4AC4SOFTWAREGLY B:11 , GLY B:13 , ILE B:14 , ILE B:15 , PHE B:33 , GLU B:34 , SER B:35 , THR B:42 , THR B:43 , ALA B:46 , ALA B:47 , GLY B:48 , MET B:49 , PRO B:173 , VAL B:174 , SER B:202 , GLY B:203 , PHE B:209 , CYS B:226 , TYR B:246 , GLY B:300 , ARG B:302 , HIS B:327 , ARG B:329 , ASN B:330 , GLY B:331 , ILE B:332 , LEU B:333 , PEO B:501 , HOH B:502 , HOH B:503 , HOH B:509 , HOH B:512 , HOH B:519 , HOH B:541BINDING SITE FOR RESIDUE FAD B 500
5AC5SOFTWAREARG B:302 , ARG B:329 , FAD B:500 , HOH B:580 , HOH B:607BINDING SITE FOR RESIDUE PEO B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1NG4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1NG4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1NG4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1NG4)

(-) Exons   (0, 0)

(no "Exon" information available for 1NG4)

(-) 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 GLYOX_BACSU | O31616 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:364
                                    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       360    
          GLYOX_BACSU     1 MKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPAIQNMKVDRFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFRIDRK 364
               SCOP domains d1ng4a1 A:1-218,A:307-364 Glycine oxidase ThiO                                                                                                                                                                            d1ng4a2 A:219-306 Glycine oxidase ThiO                                                  d1ng4a1 A:1-218,A:307-364 Glycine oxidase ThiO             SCOP domains
               CATH domains 1ng4A01 A:1-91,A:145-218,A:306-364  [code=3.50.50.60, no name defined]                     1ng4A02 A:92-144,A:219-305                           1ng4A01 A:1-91,A:145-218,A:306-364  [code=3.50.50.60, no name defined]    1ng4A02 A:92-144,A:219-305 D-Amino Acid Oxidase, subunit A, domain 2                   1ng4A01 A:1-91,A:145-218,A:306-364                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhh...eeee.......hhhhhh....hhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhh.........eeeee.hhhhhhhhhh......eeeeehhhhhhhh........eeeee......hhhhhhhhhhhhhhhh..eee......eeee....eeeee..eeeeeeeeee.hhhhhhhhhhhh......eeeeeeeeeee........eeee..eeeee....eeeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee......eeeee..eeeeeeee........hhhhhhhhhhhhhh....hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ng4 A   1 MKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPPIQNMKVDRFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFRIDRK 364
                                    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       360    

Chain B from PDB  Type:PROTEIN  Length:364
 aligned with GLYOX_BACSU | O31616 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:364
                                    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       360    
          GLYOX_BACSU     1 MKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPAIQNMKVDRFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFRIDRK 364
               SCOP domains d1ng4b1 B:1-218,B:307-364 Glycine oxidase ThiO                                                                                                                                                                            d1ng4b2 B:219-306 Glycine oxidase ThiO                                                  d1ng4b1 B:1-218,B:307-364 Glycine oxidase ThiO             SCOP domains
               CATH domains 1ng4B01 B:1-91,B:145-218,B:306-364  [code=3.50.50.60, no name defined]                     1ng4B02 B:92-144,B:219-305                           1ng4B01 B:1-91,B:145-218,B:306-364  [code=3.50.50.60, no name defined]    1ng4B02 B:92-144,B:219-305 D-Amino Acid Oxidase, subunit A, domain 2                   1ng4B01 B:1-91,B:145-218,B:306-364                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.eeee..hhhhhhhhhhhhhh...eeee.......hhhhhh....hhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhh.........eeeee.hhhhhhhhhh......eeeeehhhhhhhh........eeeee......hhhhhhhhhhhhhhhh..eee......eee.....eeeee..eeeee..eee.hhhhhhhhhhhh......eeeeeeeeeee........eeee..eeeee....eeeee...ee.......hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee......eeeee..eeeeeeee....hhhhhhhhhhhhhhhhhh....hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ng4 B   1 MKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPPIQNMKVDRFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFRIDRK 364
                                    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       360    

   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 Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NG4)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GLYOX_BACSU | O31616)
molecular function
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0043799    glycine oxidase activity    Catalysis of the reactions: (1) glycine + H2O + O2 = glyoxylate + NH3 + hydrogen peroxide; (2) D-alanine + H2O + O2 = pyruvate + NH3 + hydrogen peroxide; (3) sarcosine + H2O + O2 = glyoxylate + methylamine + hydrogen peroxide; (4) N-ethylglycine + H2O + O2 = glyoxylate + ethylamine + hydrogen peroxide.
    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.
    GO:0009635    response to herbicide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a herbicide stimulus. Herbicides are chemicals used to kill or control the growth of plants.
    GO:0009228    thiamine biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
    GO:0009229    thiamine diphosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLYOX_BACSU | O316161ng3 1ryi 3if9

(-) Related Entries Specified in the PDB File

1ng3