1NG4 - JenaLib

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Title :   STRUCTURE OF THIO (GLYCINE OXIDASE) FROM BACILLUS SUBTILIS

Authors :   E. C. Settembre, P. C. Dorrestein, J. Park, A. Augustine, T. P. Begley, S

Date :   16 Dec 02 (Deposition) - 08 Apr 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (2x)

Keywords :   Flavoprotein, Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. C. Settembre, P. C. Dorrestein, J. Park, A. Augustine, T. P. Begley, S. E. Ealick
Structural And Mechanistic Studies On Thio, A Glycine Oxidase Essential For Thiamin Biosynthesis In Bacillus Subtilis
Biochemistry V. 42 2971 2003
PubMed-ID: 12627963 | Reference-DOI: 10.1021/BI026916V

Molecule 1 - GLYCINE OXIDASE
	Chains	:	A, B
	EC Number	:	1.5.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16-B
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GOXB
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	PEO	2	Ligand/Ion	HYDROGEN PEROXIDE
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	PEO	4	Ligand/Ion	HYDROGEN PEROXIDE
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:89 , ARG A:254 , ARG B:89 , ARG B:254	BINDING SITE FOR RESIDUE PO4 B 402
2	AC2	SOFTWARE	GLY A:11 , GLY A:13 , ILE A:14 , ILE A:15 , PHE A:33 , GLU A:34 , SER A:35 , ARG A:41 , THR A:42 , THR A:43 , ALA A:46 , ALA A:47 , GLY A:48 , MET A:49 , VAL A:174 , SER A:202 , GLY A:203 , TRP A:205 , PHE A:209 , CYS A:226 , TYR A:246 , GLY A:300 , ARG A:302 , HIS A:327 , ARG A:329 , ASN A:330 , GLY A:331 , ILE A:332 , LEU A:333 , PEO A:401 , HOH A:402 , HOH A:403 , HOH A:404 , HOH A:408 , HOH A:412 , HOH A:421	BINDING SITE FOR RESIDUE FAD A 400
3	AC3	SOFTWARE	ARG A:302 , ARG A:329 , FAD A:400 , HOH A:436 , HOH A:484	BINDING SITE FOR RESIDUE PEO A 401
4	AC4	SOFTWARE	GLY B:11 , GLY B:13 , ILE B:14 , ILE B:15 , PHE B:33 , GLU B:34 , SER B:35 , THR B:42 , THR B:43 , ALA B:46 , ALA B:47 , GLY B:48 , MET B:49 , PRO B:173 , VAL B:174 , SER B:202 , GLY B:203 , PHE B:209 , CYS B:226 , TYR B:246 , GLY B:300 , ARG B:302 , HIS B:327 , ARG B:329 , ASN B:330 , GLY B:331 , ILE B:332 , LEU B:333 , PEO B:501 , HOH B:502 , HOH B:503 , HOH B:509 , HOH B:512 , HOH B:519 , HOH B:541	BINDING SITE FOR RESIDUE FAD B 500
5	AC5	SOFTWARE	ARG B:302 , ARG B:329 , FAD B:500 , HOH B:580 , HOH B:607	BINDING SITE FOR RESIDUE PEO B 501

(no "SS Bond" information available for 1NG4)

(no "Cis Peptide Bond" information available for 1NG4)

(no "SAP(SNP)/Variant" information available for 1NG4)

(no "PROSITE Motif" information available for 1NG4)

(no "Exon" information available for 1NG4)

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:364
 aligned with GLYOX_BACSU | O31616 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:364
                                    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    
          GLYOX_BACSU     1 MKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPAIQNMKVDRFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFRIDRK 364
               SCOP domains d1ng4a1 A:1-218,A:307-364 Glycine oxidase ThiO                                                                                                                                                                            d1ng4a2 A:219-306 Glycine oxidase ThiO                                                  d1ng4a1 A:1-218,A:307-364 Glycine oxidase ThiO             SCOP domains
               CATH domains 1ng4A01 A:1-91,A:145-218,A:306-364  [code=3.50.50.60, no name defined]                     1ng4A02 A:92-144,A:219-305                           1ng4A01 A:1-91,A:145-218,A:306-364  [code=3.50.50.60, no name defined]    1ng4A02 A:92-144,A:219-305 D-Amino Acid Oxidase, subunit A, domain 2                   1ng4A01 A:1-91,A:145-218,A:306-364                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhh...eeee.......hhhhhh....hhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhh.........eeeee.hhhhhhhhhh......eeeeehhhhhhhh........eeeee......hhhhhhhhhhhhhhhh..eee......eeee....eeeee..eeeeeeeeee.hhhhhhhhhhhh......eeeeeeeeeee........eeee..eeeee....eeeee...ee.......hhhhhhhhhhhhhhhhhhhhhheeeeeeeeeeee......eeeee..eeeeeeee........hhhhhhhhhhhhhh....hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ng4 A   1 MKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPPIQNMKVDRFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFRIDRK 364
                                    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

Chain B from PDB  Type:PROTEIN  Length:364
 aligned with GLYOX_BACSU | O31616 from UniProtKB/Swiss-Prot  Length:369

    Alignment length:364
                                    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    
          GLYOX_BACSU     1 MKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPAIQNMKVDRFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFRIDRK 364
               SCOP domains d1ng4b1 B:1-218,B:307-364 Glycine oxidase ThiO                                                                                                                                                                            d1ng4b2 B:219-306 Glycine oxidase ThiO                                                  d1ng4b1 B:1-218,B:307-364 Glycine oxidase ThiO             SCOP domains
               CATH domains 1ng4B01 B:1-91,B:145-218,B:306-364  [code=3.50.50.60, no name defined]                     1ng4B02 B:92-144,B:219-305                           1ng4B01 B:1-91,B:145-218,B:306-364  [code=3.50.50.60, no name defined]    1ng4B02 B:92-144,B:219-305 D-Amino Acid Oxidase, subunit A, domain 2                   1ng4B01 B:1-91,B:145-218,B:306-364                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.eeee..hhhhhhhhhhhhhh...eeee.......hhhhhh....hhhhh....hhhhhhhhhhhhhh.hhhhhhhhhhh.........eeeee.hhhhhhhhhh......eeeeehhhhhhhh........eeeee......hhhhhhhhhhhhhhhh..eee......eee.....eeeee..eeeee..eee.hhhhhhhhhhhh......eeeeeeeeeee........eeee..eeeee....eeeee...ee.......hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee......eeeee..eeeeeeee....hhhhhhhhhhhhhhhhhh....hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ng4 B   1 MKRHYEAVVIGGGIIGSAIAYYLAKENKNTALFESGTMGGRTTSAAAGMLGAHAECEERDAFFDFAMHSQRLYKGLGEELYALSGVDIRQHNGGMFKLAFSEEDVLQLRQMDDLDSVSWYSKEEVLEKEPYASGDIFGASFIQDDVHVEPYFVCKAYVKAAKMLGAEIFEHTPVLHVERDGEALFIKTPSGDVWANHVVVASGVWSGMFFKQLGLNNAFLPVKGECLSVWNDDIPLTKTLYHDHCYIVPRKSGRLVVGATMKPGDWSETPDLGGLESVMKKAKTMLPPIQNMKVDRFWAGLRPGTKDGKPYIGRHPEDSRILFAAGHFRNGILLAPATGALISDLIMNKEVNQDWLHAFRIDRK 364
                                    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

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: D-Amino Acid Oxidase; Chain A, domain 2 (80)

Homologous Superfamily: D-Amino Acid Oxidase, subunit A, domain 2 (80)

Bacillus subtilis. Organism_taxid: 1423. (4)

1a	1ng4A02	A:92-144,A:219-305
1b	1ng4B02	B:92-144,B:219-305

Architecture: 3-Layer(bba) Sandwich (528)

Topology: FAD/NAD(P)-binding domain (373)

Homologous Superfamily: [code=3.50.50.60, no name defined] (373)

Bacillus subtilis. Organism_taxid: 1423. (4)

2a	1ng4A01	A:1-91,A:145-218,A:306-364
2b	1ng4B01	B:1-91,B:145-218,B:306-364

(no "Pfam Domain" information available for 1NG4)

Asymmetric Unit(hide GO term definitions)

Chain A,B (GLYOX_BACSU | O31616)

molecular function
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0043799	glycine oxidase activity	Catalysis of the reactions: (1) glycine + H2O + O2 = glyoxylate + NH3 + hydrogen peroxide; (2) D-alanine + H2O + O2 = pyruvate + NH3 + hydrogen peroxide; (3) sarcosine + H2O + O2 = glyoxylate + methylamine + hydrogen peroxide; (4) N-ethylglycine + H2O + O2 = glyoxylate + ethylamine + hydrogen peroxide.
	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.
	GO:0009635	response to herbicide	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a herbicide stimulus. Herbicides are chemicals used to kill or control the growth of plants.
	GO:0009228	thiamine biosynthetic process	The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
	GO:0009229	thiamine diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
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
(no "Cis Peptide Bonds" information available for 1ng4)

Biological Unit
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	GLYOX_BACSU \| O31616	:	1ng3 1ryi 3if9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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