3QSE - JenaLib

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Title :   CRYSTAL STRUCTURE FOR THE COMPLEX OF SUBSTRATE-REDUCED MSOX WITH SARCOSINE

Authors :   P. Kommoju, Z. Chen, R. C. Bruckner, F. S. Mathews, M. S. Jorns

Date :   21 Feb 11 (Deposition) - 01 Jun 11 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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. R. Kommoju, Z. W. Chen, R. C. Bruckner, F. S. Mathews, M. S. Jorns
Probing Oxygen Activation Sites In Two Flavoprotein Oxidase Using Chloride As An Oxygen Surrogate.
Biochemistry V. 50 5521 2011
PubMed-ID: 21568312 | Reference-DOI: 10.1021/BI200388G
(for further references see the PDB file header)

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	:	536056
	Expression System Vector Type	:	PLASMID
	Gene	:	SOXA, SOX
	Organism Scientific	:	BACILLUS SP.
	Organism Taxid	:	69000
	Strain	:	B-0618
	Synonym	:	MSOX

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	SAR	2	Ligand/Ion	SARCOSINE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	SAR	1	Ligand/Ion	SARCOSINE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	SAR	1	Ligand/Ion	SARCOSINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY 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 , ARG A:172 , VAL A:173 , SER A:200 , MET A:201 , GLY A:202 , TRP A:204 , LEU A:208 , GLN A:223 , VAL A:225 , 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 , SAR A:401 , CL A:403 , HOH A:1036 , HOH A:1038 , HOH A:1040 , HOH A:1072 , HOH A:1741	BINDING SITE FOR RESIDUE FAD A 400
2	AC2	SOFTWARE	TYR A:317 , THR A:318 , SER A:343 , GLY A:344 , FAD A:400 , HOH A:1026	BINDING SITE FOR RESIDUE CL A 403
3	AC3	SOFTWARE	ILE A:50 , ARG A:52 , MET A:245 , TYR A:254 , HIS A:269 , TYR A:317 , GLY A:344 , HIS A:345 , LYS A:348 , FAD A:400	BINDING SITE FOR RESIDUE SAR A 401
4	AC4	SOFTWARE	TYR B:317 , THR B:318 , PHE B:342 , SER B:343 , GLY B:344 , FAD B:400 , HOH B:1015	BINDING SITE FOR RESIDUE CL B 403
5	AC5	SOFTWARE	GLY 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 , GLN B:223 , VAL B:225 , 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 , SAR B:401 , CL B:403 , HOH B:1020 , HOH B:1035 , HOH B:1061 , HOH B:1099 , HOH B:1112	BINDING SITE FOR RESIDUE FAD B 400
6	AC6	SOFTWARE	ILE B:50 , ARG B:52 , TYR B:254 , HIS B:269 , TYR B:317 , GLY B:344 , HIS B:345 , LYS B:348 , FAD B:400	BINDING SITE FOR RESIDUE SAR B 401

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

Asymmetric Unit

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

(no "SAP(SNP)/Variant" information available for 3QSE)

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

(no "Exon" information available for 3QSE)

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 d3qsea1 A:1-217,A:322-385 Sarcosine oxidase                                                                                                                                                                              d3qsea2 A:218-321 Sarcosine oxidase                                                                     d3qsea1 A:1-217,A:322-385 Sarcosine oxidase                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhh....eeee................eee......hhhhhhhhhhhhhhhhhhhhhh....ee...eeeeee...hhhhhhhhhhhhhhh...eeeehhhhhhhh........eeeeee...eeehhhhhhhhhhhhhhhh..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
                 3qse 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

Chain B from PDB  Type:PROTEIN  Length:382
 aligned with MSOX_BACB0 | P40859 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:382
                                    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 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKE 383
               SCOP domains d3qseb1 B:1-217,B:322-382 Sarcosine oxidase                                                                                                                                                                              d3qseb2 B:218-321 Sarcosine oxidase                                                                     d3qseb1 B:1-217,B:322-382 Sarcosine oxidase                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----DAO-3qseB01 B:5-360                                                                                                                                                                                                                                                                                                                                                 ---------------------- Pfam domains (1)
           Pfam domains (2) ----DAO-3qseB02 B:5-360                                                                                                                                                                                                                                                                                                                                                 ---------------------- Pfam domains (2)
         Sec.struct. author ..eeeeeee..hhhhhhhhhhhhh....eeee...............eeee......hhhhhhhhhhhhhhhhhhhhhh....ee...eeeeee...hhhhhhhhhhhhhh....eeeehhhhhhhh........eeeeee...eeeehhhhhhhhhhhhhhh..eee....eeeeeee..eeeeee...eeeeeeeee.hhhhhhhhhhhhh.....eeeeeeeeee..hhhhhhhhhh..eeeeee..eeeeee.......eeeee....ee.............hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee......eeeee..eeeeeeee.....hhhhhhhhhhhhhhhhhhh.....hhhhh..hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qse B   1 STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKE 382
                                    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 '\|'

(no "CATH Domain" information available for 3QSE)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: DAO (25)

Bacillus sp. (strain B-0618) (9)

1a	DAO-3qseB01	B:5-360
1b	DAO-3qseB02	B:5-360

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Pro A:37 - Pro A:38	[ RasMol ]
		Pro B:37 - Pro B:38	[ RasMol ]

Biological Units
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	3qse
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1l9f	MONOMERIC SARCOSINE OXIDASE: STRUCTURE OF A COVALENTLY FLAVINYLATED AMINE OXIDIZING ENZYME
3qsm
3qss

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (2, 4)

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