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(-) Description

Title :  COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR PYRROLE-2-CARBOXYLATE
 
Authors :  M. A. Wagner, P. Trickey, Z. -W. Chen, F. S. Mathews, M. S. Jorns
Date :  13 Mar 00  (Deposition) - 06 Dec 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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 :  M. A. Wagner, P. Trickey, Z. W. Chen, F. S. Mathews, M. S. Jorns
Monomeric Sarcosine Oxidase: 1. Flavin Reactivity And Activ Site Binding Determinants.
Biochemistry V. 39 8813 2000
PubMed-ID: 10913292  |  Reference-DOI: 10.1021/BI000349Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SARCOSINE OXIDASE
    ChainsA, B
    EC Number1.5.3.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System CellDH1 CELLS
    Expression System Taxid562
    Organism ScientificBACILLUS SP.
    Organism Taxid69000
    StrainB-0618

 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  (5, 24)

Asymmetric Unit (5, 24)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MSE14Mod. Amino AcidSELENOMETHIONINE
4PO43Ligand/IonPHOSPHATE ION
5PYC3Ligand/IonPYRROLE-2-CARBOXYLATE
Biological Unit 1 (4, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MSE7Mod. Amino AcidSELENOMETHIONINE
4PO41Ligand/IonPHOSPHATE ION
5PYC1Ligand/IonPYRROLE-2-CARBOXYLATE
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3MSE7Mod. Amino AcidSELENOMETHIONINE
4PO42Ligand/IonPHOSPHATE ION
5PYC2Ligand/IonPYRROLE-2-CARBOXYLATE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:81 , ASN A:151 , ARG A:154 , HOH A:901BINDING SITE FOR RESIDUE PO4 A 803
02AC2SOFTWARETHR A:318 , PHE A:342 , SER A:343 , GLY A:344 , FAD A:400BINDING SITE FOR RESIDUE CL A 804
03AC3SOFTWAREHIS 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:911 , HOH B:1129BINDING SITE FOR RESIDUE PO4 B 812
04AC4SOFTWAREHIS B:81 , ASN B:151 , ARG B:154 , HOH B:824 , HOH B:1115BINDING SITE FOR RESIDUE PO4 B 813
05AC5SOFTWARETYR B:317 , THR B:318 , GLY B:344 , FAD B:400 , HOH B:872BINDING SITE FOR RESIDUE CL B 814
06AC6SOFTWAREGLY A:10 , GLY A:12 , SER A:13 , MSE 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 , MSE A:201 , GLY A:202 , TRP A:204 , LEU A:208 , VAL A:225 , TYR A:254 , CYS A:315 , MSE A:316 , TYR A:317 , PHE A:342 , GLY A:344 , HIS A:345 , GLY A:346 , PHE A:347 , LYS A:348 , PYC A:801 , CL A:804 , HOH A:814 , HOH A:820 , HOH A:825 , HOH A:858 , HOH A:889 , HOH A:934BINDING SITE FOR RESIDUE FAD A 400
07AC7SOFTWAREILE A:50 , ARG A:52 , MSE A:245 , TYR A:254 , HIS A:269 , TYR A:317 , GLY A:344 , HIS A:345 , LYS A:348 , FAD A:400BINDING SITE FOR RESIDUE PYC A 801
08AC8SOFTWAREGLY B:10 , GLY B:12 , SER B:13 , MSE 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 , MSE B:201 , GLY B:202 , TRP B:204 , LEU B:208 , VAL B:225 , TYR B:254 , CYS B:315 , MSE B:316 , TYR B:317 , PHE B:342 , GLY B:344 , HIS B:345 , GLY B:346 , PHE B:347 , LYS B:348 , PYC B:811 , CL B:814 , HOH B:821 , HOH B:823 , HOH B:826 , HOH B:827 , HOH B:868BINDING SITE FOR RESIDUE FAD B 400
09AC9SOFTWAREILE B:50 , ARG B:52 , MSE B:245 , TYR B:254 , HIS B:269 , TYR B:317 , GLY B:344 , HIS B:345 , LYS B:348 , FAD B:400BINDING SITE FOR RESIDUE PYC B 811
10BC1SOFTWAREPRO B:217 , GLN B:219 , TYR B:221 , LYS B:319 , THR B:320 , LEU B:321 , HOH B:936 , HOH B:1021BINDING SITE FOR RESIDUE PYC B 815

(-) SS Bonds  (0, 0)

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

(-) 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 1ELI)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1ELI)

(-) 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 d1elia1 A:1-217,A:322-385 Sarcosine oxidase                                                                                                                                                                              d1elia2 A:218-321 Sarcosine oxidase                                                                     d1elia1 A:1-217,A:322-385 Sarcosine oxidase                      SCOP domains
               CATH domains 1eliA01 A:1-59,A:149-212,A:326-378                         1eliA02 A:60-145,A:213-321 D-Amino Acid Oxidase, subunit A, domain 2                  ---1eliA01 A:1-59,A:149-212,A:326-378                              1eliA02 A:60-145,A:213-321 D-Amino Acid Oxidase, subunit A, domain 2                                         ----1eliA01 A:1-59,A:149-212,A:326-378                   ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..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
                 1eli A   1 STHFDVIVVGAGSmGmAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETmEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSmGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFmVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYmPGANGELKRGAVCmYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQ 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     
                                        14-MSE                                                                                    105-MSE                                                                                         201-MSE                                     245-MSE                                                  302-MSE       316-MSE                                                                 
                                          16-MSE                                                                                                                                                                                                                                                                                                                                                                             

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 d1elib1 B:1-217,B:322-385 Sarcosine oxidase                                                                                                                                                                              d1elib2 B:218-321 Sarcosine oxidase                                                                     d1elib1 B:1-217,B:322-385 Sarcosine oxidase                      SCOP domains
               CATH domains 1eliB01 B:1-59,B:149-212,B:326-378                         1eliB02 B:60-145,B:213-321 D-Amino Acid Oxidase, subunit A, domain 2                  ---1eliB01 B:1-59,B:149-212,B:326-378                              1eliB02 B:60-145,B:213-321 D-Amino Acid Oxidase, subunit A, domain 2                                         ----1eliB01 B:1-59,B:149-212,B:326-378                   ------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhhhhhh...eeee................eee......hhhhhhhhhhhhhhhhhhhhhh....ee...eeeeee...hhhhhhhhhhhhhh....eeeehhhhhhhh........eeeeee...eeehhhhhhhhhhhhhhhh..eee.......eeee..eeee......eeeeeeee.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
                 1eli B   1 STHFDVIVVGAGSmGmAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETmEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSmGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFmVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYmPGANGELKRGAVCmYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQ 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     
                                        14-MSE                                                                                    105-MSE                                                                                         201-MSE                                     245-MSE                                                  302-MSE       316-MSE                                                                 
                                          16-MSE                                                                                                                                                                                                                                                                                                                                                                             

   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 1ELI)

(-) 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 | P408591el5 1el7 1el8 1el9 1l9c 1l9d 1l9e 2a89 2gb0 2gf3 3bhf 3bhk 3m0o 3m12 3m13 3qse 3qsm 3qss

(-) Related Entries Specified in the PDB File

1b3m MONOMERIC SARCOSINE OXIDASE: STRUCTURE OF A COVALENTLY FLAVINYLATED AMINE OXIDIZING ENZYME
1el5 MONOMERIC SARCOSINE OXIDASE WITH DIMETHYLGLYCINE
1el7 MONOMERIC SARCOSINE OXIDASE WITH [METHYLTELLURO]ACETATE
1el8 MONOMERIC SARCOSINE OXIDASE WITH [METHYLSELENO]ACETATE
1el9 MONOMERIC SARCOSINE OXIDASE WITH [METHYLTHIO]ACETATE