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(-) Description

Title :  CRYSTAL STRUCTURE OF R49K MUTANT OF MONOMERIC SARCOSINE OXIDASE CRYSTALLIZED IN PHOSPHATE AS PRECIPITANT
 
Authors :  A. Hassan-Abdallah, G. Zhao, Z. Chen, F. S. Mathews, M. S. Jorns
Date :  28 Nov 07  (Deposition) - 26 Feb 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.71
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Flavoprotein Oxidase, Fad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Hassan-Abdallah, G. Zhao, Z. W. Chen, F. S. Mathews, M. Schuman Jorns
Arginine 49 Is A Bifunctional Residue Important In Catalysi And Biosynthesis Of Monomeric Sarcosine Oxidase: A Context-Sensitive Model For The Electrostatic Impact Of Arginine To Lysine Mutations.
Biochemistry V. 47 2913 2008
PubMed-ID: 18251505  |  Reference-DOI: 10.1021/BI702351V
(for further references see the PDB file header)

(-) 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
    Mutation: YES
    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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL2Ligand/IonGLYCEROL
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL1Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:317 , THR A:318 , SER A:343 , GLY A:344 , HOH A:923BINDING SITE FOR RESIDUE CL A 401
2AC2SOFTWARETYR B:317 , THR B:318 , SER B:343 , GLY B:344 , HOH B:1127BINDING SITE FOR RESIDUE CL B 401
3AC3SOFTWAREGLY A:10 , GLY A:12 , SER A:13 , MET A:14 , ASP A:33 , ALA A:34 , PHE A:35 , HIS A:39 , GLY A:42 , SER A:43 , HIS A:44 , LYS A:49 , ILE A:50 , THR A:171 , ARG A:172 , 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 , HOH A:907 , HOH A:914 , HOH A:915 , HOH A:933 , HOH A:935 , HOH A:959 , HOH A:1051BINDING SITE FOR RESIDUE FAD A 400
4AC4SOFTWAREGLY B:10 , GLY B:12 , SER B:13 , MET B:14 , ASP B:33 , ALA B:34 , PHE B:35 , HIS B:39 , GLY B:42 , SER B:43 , HIS B:44 , LYS B:49 , ILE B:50 , THR B:171 , ARG B:172 , 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 , HOH B:1111 , HOH B:1112 , HOH B:1114 , HOH B:1121 , HOH B:1148 , HOH B:1166BINDING SITE FOR RESIDUE FAD B 400
5AC5SOFTWARELYS A:86 , ASN A:237 , ASP A:240 , HOH A:951 , HOH A:973 , HOH A:1128 , HOH A:1159 , GLU B:78 , LEU B:159BINDING SITE FOR RESIDUE GOL A 901
6AC6SOFTWAREGLU A:78 , LEU A:159 , HOH A:955 , LYS B:86 , ASN B:237 , ASP B:240 , HOH B:1142 , HOH B:1196 , HOH B:1250 , HOH B:1413BINDING SITE FOR RESIDUE GOL B 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BHK)

(-) 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 3BHK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BHK)

(-) Exons   (0, 0)

(no "Exon" information available for 3BHK)

(-) 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:385
 aligned with MSOX_BACB0 | P40859 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:385
                                    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 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQ 386
               SCOP domains d3bhka1 A:1-217,A:322-381 Sarcosine oxidase                                                                                                                                                                              d3bhka2 A:218-321 Sarcosine oxidase                                                                     d3bhka1 A:1-217,A:322-381 Sarcosine oxidase                 ---- SCOP domains
               CATH domains 3bhkA01 A:1-59,A:149-212,A:326-385                         3bhkA02 A:60-145,A:213-321 D-Amino Acid Oxidase, subunit A, domain 2                  ---3bhkA01 A:1-59,A:149-212,A:326-385                              3bhkA02 A:60-145,A:213-321 D-Amino Acid Oxidase, subunit A, domain 2                                         ----3bhkA01 A:1-59,A:149-212,A:326-385                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhhh...eeee...............eeee......hhhhhhhhhhhhhhhhhhhhhh....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
                 3bhk A   1 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTKIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQ 385
                                    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:385
 aligned with MSOX_BACB0 | P40859 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:385
                                    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 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQ 386
               SCOP domains d3bhkb1 B:1-217,B:322-381 Sarcosine oxidase                                                                                                                                                                              d3bhkb2 B:218-321 Sarcosine oxidase                                                                     d3bhkb1 B:1-217,B:322-381 Sarcosine oxidase                 ---- SCOP domains
               CATH domains 3bhkB01 B:1-59,B:149-212,B:326-385                         3bhkB02 B:60-145,B:213-321 D-Amino Acid Oxidase, subunit A, domain 2                  ---3bhkB01 B:1-59,B:149-212,B:326-385                              3bhkB02 B:60-145,B:213-321 D-Amino Acid Oxidase, subunit A, domain 2                                         ----3bhkB01 B:1-59,B:149-212,B:326-385                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhh...eeee...............eeee......hhhhhhhhhhhhhhhhhhhhhh....ee...eeeeee...hhhhhhhhhhhhhh....eeeehhhhhhhh........eeeeee...eeeehhhhhhhhhhhhhhh..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
                 3bhk B   1 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTKIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQ 385
                                    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 3BHK)

(-) 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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  1.5.3.1
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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 2gb0 2gf3 3bhf 3m0o 3m12 3m13 3qse 3qsm 3qss

(-) Related Entries Specified in the PDB File

1l9f MONOMERIC SARCOSINE OXIDASE: STRUCTURE OF A COVALENTLY FLAVINYLATED AMINE OXIDIZING ENZYME
3bhf SAME PROTEIN COMPLEXED WITH FAD, CL