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(-) Description

Title :  CRYSTAL STRUCTURE OF DIMETHYLGLYCINE OXIDASE OF ARTHROBACTER GLOBIFORMIS IN COMPLEX WITH FOLIC ACID
 
Authors :  D. Leys, J. Basran, N. S. Scrutton
Date :  01 Jun 03  (Deposition) - 07 Oct 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  A  (1x)
Keywords :  Channelling, Folate Binding, Fad Binding, Amine Oxidation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Leys, J. Basran, N. S. Scrutton
Channelling And Formation Of 'Active' Formaldehyde In Dimethylglycine Oxidase.
Embo J. V. 22 4038 2003
PubMed-ID: 12912903  |  Reference-DOI: 10.1093/EMBOJ/CDG395

(-) Compounds

Molecule 1 - N,N-DIMETHYLGLYCINE OXIDASE
    Chains: A
    EC Number: 1.5.3.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTHROBACTER GLOBIFORMIS
    Organism Taxid: 1665

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A
Biological Unit 2 (1x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FOL1Ligand/IonFOLIC ACID
3NA1Ligand/IonSODIUM ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FOL4Ligand/IonFOLIC ACID
3NA-1Ligand/IonSODIUM ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2FOL1Ligand/IonFOLIC ACID
3NA-1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:257 , VAL A:412 , HOH A:2944 , HOH A:3153 , HOH A:3552BINDING SITE FOR RESIDUE NA A 2001
2AC2SOFTWARELEU A:508 , TYR A:539 , THR A:554 , TYR A:631 , PHE A:632 , LEU A:649 , TYR A:651 , GLU A:658 , TYR A:699 , HOH A:2971 , HOH A:2987 , HOH A:3177 , HOH A:3240 , HOH A:3265 , HOH A:3374 , HOH A:3674 , HOH A:3701 , HOH A:3929BINDING SITE FOR RESIDUE FOL A 2887
3AC3SOFTWAREGLY A:11 , GLY A:13 , ILE A:14 , VAL A:15 , ASP A:35 , GLN A:36 , PRO A:42 , GLY A:44 , SER A:45 , THR A:46 , HIS A:48 , ALA A:49 , PRO A:50 , GLY A:51 , LEU A:52 , THR A:172 , VAL A:174 , CYS A:202 , ALA A:203 , GLY A:204 , TRP A:206 , ILE A:210 , HIS A:225 , TYR A:259 , GLY A:333 , ILE A:334 , VAL A:360 , TRP A:361 , VAL A:362 , THR A:363 , HOH A:2909 , HOH A:2911 , HOH A:2912 , HOH A:2915 , HOH A:2945 , HOH A:2992 , HOH A:3010 , HOH A:3143BINDING SITE FOR RESIDUE FAD A 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PJ6)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gln A:242 -Pro A:243
2Ser A:426 -Pro A:427
3Asp A:818 -Pro A:819

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PJ6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PJ6)

(-) Exons   (0, 0)

(no "Exon" information available for 1PJ6)

(-) 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:828
 aligned with DMGO_ARTGO | Q9AGP8 from UniProtKB/Swiss-Prot  Length:830

    Alignment length:828
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822        
           DMGO_ARTGO     3 STPRIVIIGAGIVGTNLADELVTRGWNNITVLDQGPLNMPGGSTSHAPGLVFQTNPSKTMASFAKYTVEKLLSLTEDGVSCFNQVGGLEVATTETRLADLKRKLGYAAAWGIEGRLLSPAECQELYPLLDGENILGGLHVPSDGLASAARAVQLLIKRTESAGVTYRGSTTVTGIEQSGGRVTGVQTADGVIPADIVVSCAGFWGAKIGAMIGMAVPLLPLAHQYVKTTPVPAQQGRNDQPNGARLPILRHQDQDLYYREHGDRYGIGSYAHRPMPVDVDTLGAYAPETVSEHHMPSRLDFTLEDFLPAWEATKQLLPALADSEIEDGFNGIFSFTPDGGPLLGESKELDGFYVAEAVWVTHSAGVAKAMAELLTTGRSETDLGECDITRFEDVQLTPEYVSETSQQNFVEIYDVLHPLQPRLSPRNLRVSPFHARHKELGAFFLEAGGWERPYWFEANAALLKEMPAEWLPPARDAWSGMFSSPIAAAEAWKTRTAVAMYDMTPLKRLEVSGPGALKLLQELTTADLAKKPGAVTYTLLLDHAGGVRSDITVARLSEDTFQLGANGNIDTAYFERAARHQTQSGSATDWVQVRDTTGGTCCIGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGELGWELYTSADNGQRLWDALWQAGQPFGVIAAGRAAFSSLRLEKGYRSWGTDMTTEHDPFEAGLGFAVKMAKESFIGKGALEGRTEEASARRLRCLTIDDGRSIVLGKEPVFYKEQAVGYVTSAAYGYTVAKPIAYSYLPGTVSVGDSVDIEYFGRRITATVTEDPLYDPKMTRLRG 830
               SCOP domains d1pj6a2 A:3-219,A:339-427 N,N-dimethylglycine oxidase                                                                                                                                                                    d1pj6a3 A:220-338 N,N-dimethylglycine oxidase                                                                          d1pj6a2 A:3-219,A:339-427 N,N-dimethylglycine oxidase                                    d1pj6a4 A:428-742 N,N-dimethylglycine oxidase domain 3                                                                                                                                                                                                                                                                     d1pj6a1 A:743-830 N,N-dimethylglycine oxidase, C-terminal domain                         SCOP domains
               CATH domains 1pj6A01 A:3-85,A:145-219,A:339-421  [code=3.50.50.60, no name defined]             1pj6A02 A:86-144,A:220-338                                 1pj6A01 A:3-85,A:145-219,A:339-421  [code=3.50.50.60, no name defined]     1pj6A02 A:86-144,A:220-338 D-Amino Acid Oxidase, subunit A, domain 2                                                   1pj6A01 A:3-85,A:145-219,A:339-421  [code=3.50.50.60, no name defined]             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1pj6A05 A:740-817 Aminomethyltransferase beta-barrel domains                  ------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh....eeee.........hhhhhh..ee.....hhhhhhhhhhhhhhhhhhee..ee.ee...eeeee.hhhhhhhhhhhhhhhhhhh...eeehhhhhhhhh...hhhhh.eeeee...eeehhhhhhhhhhhhhhhh..eee....eeeeeee..eeeeeee..eeee..eeee.hhhhhhhhhhh.......eeeeeeeeee..hhhhh............eeeehhh.eeeeee..eeeeee........hhhhh...hhhhh.......ee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee......eeee......eeeee..hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhh.eeeeee..eeeeeee.hhhhhhhhhhhhhh.............hhhhhhhhhhhhh.eeee....eeeeee..hhhhhhhhhh..........eeeeeee.....eeeeeeeeeee..eeeeee.hhhhhhhhhhhhhhhhhhh......eeee....eeeeeee..hhhhhhh................eeeeee..eeeeee........eeeeeee..hhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhh...................hhhhh.........hhhhh........eeeeeeee...........eeee..eeeeeeeeeeee....eeeeeeeee.......eeeeee..eeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pj6 A   3 STPRIVIIGAGIVGTNLADELVTRGWNNITVLDQGPLNMPGGSTSHAPGLVFQTNPSKTMASFAKYTVEKLLSLTEDGVSCFNQVGGLEVATTETRLADLKRKLGYAAAWGIEGRLLSPAECQELYPLLDGENILGGLHVPSDGLASAARAVQLLIKRTESAGVTYRGSTTVTGIEQSGGRVTGVQTADGVIPADIVVSCAGFWGAKIGAMIGMAVPLLPLAHQYVKTTPVPAQQGRNDQPNGARLPILRHQDQDLYYREHGDRYGIGSYAHRPMPVDVDTLGAYAPETVSEHHMPSRLDFTLEDFLPAWEATKQLLPALADSEIEDGFNGIFSFTPDGGPLLGESKELDGFYVAEAVWVTHSAGVAKAMAELLTTGRSETDLGECDITRFEDVQLTPEYVSETSQQNFVEIYDVLHPLQPRLSPRNLRVSPFHARHKELGAFFLEAGGWERPYWFEANAALLKEMPAEWLPPARDAWSGMFSSPIAAAEAWKTRTAVAMYDMTPLKRLEVSGPGALKLLQELTTADLAKKPGAVTYTLLLDHAGGVRSDITVARLSEDTFQLGANGNIDTAYFERAARHQTQSGSATDWVQVRDTTGGTCCIGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGELGWELYTSADNGQRLWDALWQAGQPFGVIAAGRAAFSSLRLEKGYRSWGTDMTTEHDPFEAGLGFAVKMAKESFIGKGALEGRTEEASARRLRCLTIDDGRSIVLGKEPVFYKEQAVGYVTSAAYGYTVAKPIAYSYLPGTVSVGDSVDIEYFGRRITATVTEDPLYDPKMTRLRG 830
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822
   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  (4, 4)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PJ6)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A   (DMGO_ARTGO | Q9AGP8)
molecular function
    GO:0047866    dimethylglycine oxidase activity    Catalysis of the reaction: N,N-dimethylglycine + H(2)O + O(2) = formaldehyde + H(2)O(2) + sarcosine.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.

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  1.5.3.10
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 Related Entries

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

UniProtKB/Swiss-Prot
        DMGO_ARTGO | Q9AGP8: 1pj5 1pj7 3gsi

(-) Related Entries Specified in the PDB File

1pj5 DIMETHYLGLYCINE OXIDASE IN COMPLEX WITH ACETATE
1pj7