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(-) Description

Title :  MONOMERIC SARCOSINE OXIDASE: STRUCTURE OF A COVALENTLY FLAVINYLATED AMINE OXIDIZING ENZYME
 
Authors :  P. Trickey, M. A. Wagner, M. S. Jorns, F. S. Mathews
Date :  09 Mar 06  (Deposition) - 21 Mar 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Flavoprotein Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Trickey, M. A. Wagner, M. S. Jorns, F. S. Mathews
Monomeric Sarcosine Oxidase: Structure Of A Covalently Flavinylated Amine Oxidizing Enzyme
Structure V. 7 331 1999
PubMed-ID: 10368302  |  Reference-DOI: 10.1016/S0969-2126(99)80043-4

(-) Compounds

Molecule 1 - MONOMERIC SARCOSINE OXIDASE
    Chains: A, B
    EC Number: 1.5.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: DH1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SOXA, SOX
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 69000
    Strain: B-0618
    Synonym: MSOX

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3PO44Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3PO41Ligand/IonPHOSPHATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3PO43Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:81 , ASN A:151 , ARG A:154 , HOH A:840BINDING SITE FOR RESIDUE PO4 A 801
2AC2SOFTWARETHR A:2 , LYS A:28 , SER B:1 , HOH B:1018 , HOH B:1064 , HOH B:1127BINDING SITE FOR RESIDUE PO4 B 802
3AC3SOFTWARETHR A:318 , GLY A:344 , FAD A:400 , HOH A:1109BINDING SITE FOR RESIDUE CL A 803
4AC4SOFTWAREHIS B:81 , ASN B:151 , ARG B:154 , HOH B:807 , HOH B:965BINDING SITE FOR RESIDUE PO4 B 804
5AC5SOFTWAREHIS B:53 , LEU B:113 , THR B:114 , VAL B:115 , GLU B:141 , PRO B:142 , ASN B:143 , SER B:144 , HOH B:917 , HOH B:1129BINDING SITE FOR RESIDUE PO4 B 805
6AC6SOFTWARETYR B:317 , THR B:318 , GLY B:344 , FAD B:400 , HOH B:1099BINDING SITE FOR RESIDUE CL B 806
7AC7SOFTWAREGLY A:10 , GLY A:12 , SER A:13 , MET A:14 , VAL A:32 , ASP A:33 , ALA A:34 , PHE A:35 , HIS A:39 , GLY A:42 , SER A:43 , HIS A:44 , ARG A:49 , ILE A:50 , THR A:171 , ARG A:172 , VAL A:173 , SER A:200 , MET A:201 , GLY A:202 , TRP A:204 , LEU A:208 , TYR A:254 , CYS A:315 , MET A:316 , TYR A:317 , PHE A:342 , GLY A:344 , HIS A:345 , GLY A:346 , PHE A:347 , LYS A:348 , CL A:803 , HOH A:809 , HOH A:824 , HOH A:825 , HOH A:873 , HOH A:894 , HOH A:896BINDING SITE FOR RESIDUE FAD A 400
8AC8SOFTWAREGLY B:10 , GLY B:12 , SER B:13 , MET B:14 , VAL B:32 , ASP B:33 , ALA B:34 , PHE B:35 , HIS B:39 , GLY B:42 , SER B:43 , HIS B:44 , ARG B:49 , ILE B:50 , THR B:171 , ARG B:172 , VAL B:173 , SER B:200 , MET B:201 , GLY B:202 , TRP B:204 , LEU B:208 , TYR B:254 , CYS B:315 , MET B:316 , TYR B:317 , PHE B:342 , GLY B:344 , HIS B:345 , GLY B:346 , PHE B:347 , LYS B:348 , CL B:806 , HOH B:812 , HOH B:814 , HOH B:825 , HOH B:836 , HOH B:838 , HOH B:998BINDING SITE FOR RESIDUE FAD B 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GB0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Pro A:37 -Pro A:38
2Pro B:37 -Pro B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GB0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GB0)

(-) Exons   (0, 0)

(no "Exon" information available for 2GB0)

(-) 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:387
 aligned with MSOX_BACB0 | P40859 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:387
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       
           MSOX_BACB0     2 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQKT 388
               SCOP domains d2gb0a1 A:1-217,A:322-387 Sarcosine oxidase                                                                                                                                                                              d2gb0a2 A:218-321 Sarcosine oxidase                                                                     d2gb0a1 A:1-217,A:322-387 Sarcosine oxidase                        SCOP domains
               CATH domains 2gb0A01 A:1-59,A:149-212,A:326-387                         2gb0A02 A:60-145,A:213-321 D-Amino Acid Oxidase, subunit A, domain 2                  ---2gb0A01 A:1-59,A:149-212,A:326-387                              2gb0A02 A:60-145,A:213-321 D-Amino Acid Oxidase, subunit A, domain 2                                         ----2gb0A01 A:1-59,A:149-212,A:326-387                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhh...eeee...............eeee........hhhhhhhhhhhhhhhhhhhh....ee...eeeeee...hhhhhhhhhhhhhh....eeeehhhhhhhh........eeeeee...eeeehhhhhhhhhhhhhhh..eee....eeeeeee..eeeeee..eeeeeeeeee.hhhhhhhhhhhh.ee...eeeeeeeeee..hhhhhhhhhh..eeeeee..eeeeee.......eeeee....ee.............hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee......eeeee..eeeeeeee.....hhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhh.ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gb0 A   1 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQKT 387
                                    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       370       380       


Chain B from PDB  Type:PROTEIN  Length:389
 aligned with MSOX_BACB0 | P40859 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:389
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381         
           MSOX_BACB0     2 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQKTTI 390
               SCOP domains d2gb0b1 B:1-217,B:322-389 Sarcosine oxidase                                                                                                                                                                              d2gb0b2 B:218-321 Sarcosine oxidase                                                                     d2gb0b1 B:1-217,B:322-389 Sarcosine oxidase                          SCOP domains
               CATH domains 2gb0B01 B:1-59,B:149-212,B:326-389                         2gb0B02 B:60-145,B:213-321 D-Amino Acid Oxidase, subunit A, domain 2                  ---2gb0B01 B:1-59,B:149-212,B:326-389                              2gb0B02 B:60-145,B:213-321 D-Amino Acid Oxidase, subunit A, domain 2                                         ----2gb0B01 B:1-59,B:149-212,B:326-389                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhh...eeee................eee......hhhhhhhhhhhhhhhhhhhhhh....ee...eeeeee...hhhhhhhhhhhhhh....eeeehhhhhhhh........eeeeee...eeehhhhhhhhhhhhhhhh..eee.......eeee..eeeeee..eeeeeeeeee.hhhhhhhhhhhh.ee...eeeeeeeeee..hhhhhhhhhh..eeeeee..eeeeee.......eeeee....ee.............hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee......eeeee..eeeeeeee.....hhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhh.ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gb0 B   1 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQKTTI 389
                                    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       370       380
   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
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GB0)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MSOX_BACB0 | P40859)
molecular function
    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:0008115    sarcosine oxidase activity    Catalysis of the reaction: H(2)O + O(2) + sarcosine = formaldehyde + glycine + H(2)O(2).
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:0046653    tetrahydrofolate metabolic process    The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
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
        MSOX_BACB0 | P40859: 1el5 1el7 1el8 1el9 1eli 1l9c 1l9d 1l9e 2a89 2gf3 3bhf 3bhk 3m0o 3m12 3m13 3qse 3qsm 3qss

(-) Related Entries Specified in the PDB File

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