1PJ5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF DIMETHYLGLYCINE OXIDASE OF ARTHROBACTER GLOBIFORMIS IN COMPLEX WITH ACETATE

Authors :   D. Leys, J. Basran, N. S. Scrutton

Date :   01 Jun 03 (Deposition) - 07 Oct 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.61

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Channelling, Fad Binding, Folate Binding, Amine Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Leys, J. Basran, N. S. Scrutton
Channelling And Formation Of 'Active' Formaldehyde In Dimethylglycine Oxidase.
Embo J. V. 22 4038 2003
PubMed-ID: 12912903 | Reference-DOI: 10.1093/EMBOJ/CDG395
(for further references see the PDB file header)

Molecule 1 - N,N-DIMETHYLGLYCINE OXIDASE
	Chains	:	A
	EC Number	:	1.5.3.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PUC19
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ARTHROBACTER GLOBIFORMIS
	Organism Taxid	:	1665

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	FAD	4	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:257 , VAL A:412 , HOH A:2147 , HOH A:2152 , HOH A:2198 , HOH A:2237	BINDING SITE FOR RESIDUE NA A 2001
2	AC2	SOFTWARE	PHE A:54 , ARG A:252 , TYR A:272 , TRP A:361 , TYR A:415 , FAD A:902 , HOH A:2313	BINDING SITE FOR RESIDUE ACT A 2145
3	AC3	SOFTWARE	GLY A:11 , GLY A:13 , ILE A:14 , VAL A:15 , ASP A:35 , GLN A:36 , PRO A:42 , GLY A:44 , SER A:45 , THR A:46 , HIS A:48 , ALA A:49 , PRO A:50 , GLY A:51 , LEU A:52 , THR A:172 , THR A:173 , VAL A:174 , CYS A:202 , ALA A:203 , GLY A:204 , TRP A:206 , ILE A:210 , HIS A:225 , TYR A:259 , GLY A:333 , ILE A:334 , PHE A:335 , VAL A:360 , TRP A:361 , VAL A:362 , THR A:363 , ACT A:2145 , HOH A:2153 , HOH A:2157 , HOH A:2170 , HOH A:2194 , HOH A:2203 , HOH A:2291 , HOH A:2399 , HOH A:2404	BINDING SITE FOR RESIDUE FAD A 902

(no "SS Bond" information available for 1PJ5)

Asymmetric Unit

No.	Residues
1	Gln A:242	-	Pro A:243
2	Ser A:426	-	Pro A:427
3	Asp A:818	-	Pro A:819

(no "SAP(SNP)/Variant" information available for 1PJ5)

(no "PROSITE Motif" information available for 1PJ5)

(no "Exon" information available for 1PJ5)

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
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Chain A from PDB  Type:PROTEIN  Length:827
 aligned with DMGO_ARTGO | Q9AGP8 from UniProtKB/Swiss-Prot  Length:830

    Alignment length:827
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823       
           DMGO_ARTGO     4 TPRIVIIGAGIVGTNLADELVTRGWNNITVLDQGPLNMPGGSTSHAPGLVFQTNPSKTMASFAKYTVEKLLSLTEDGVSCFNQVGGLEVATTETRLADLKRKLGYAAAWGIEGRLLSPAECQELYPLLDGENILGGLHVPSDGLASAARAVQLLIKRTESAGVTYRGSTTVTGIEQSGGRVTGVQTADGVIPADIVVSCAGFWGAKIGAMIGMAVPLLPLAHQYVKTTPVPAQQGRNDQPNGARLPILRHQDQDLYYREHGDRYGIGSYAHRPMPVDVDTLGAYAPETVSEHHMPSRLDFTLEDFLPAWEATKQLLPALADSEIEDGFNGIFSFTPDGGPLLGESKELDGFYVAEAVWVTHSAGVAKAMAELLTTGRSETDLGECDITRFEDVQLTPEYVSETSQQNFVEIYDVLHPLQPRLSPRNLRVSPFHARHKELGAFFLEAGGWERPYWFEANAALLKEMPAEWLPPARDAWSGMFSSPIAAAEAWKTRTAVAMYDMTPLKRLEVSGPGALKLLQELTTADLAKKPGAVTYTLLLDHAGGVRSDITVARLSEDTFQLGANGNIDTAYFERAARHQTQSGSATDWVQVRDTTGGTCCIGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGELGWELYTSADNGQRLWDALWQAGQPFGVIAAGRAAFSSLRLEKGYRSWGTDMTTEHDPFEAGLGFAVKMAKESFIGKGALEGRTEEASARRLRCLTIDDGRSIVLGKEPVFYKEQAVGYVTSAAYGYTVAKPIAYSYLPGTVSVGDSVDIEYFGRRITATVTEDPLYDPKMTRLRG 830
               SCOP domains d1pj5a2 A:4-219,A:339-427 N,N-dimethylglycine oxidase                                                                                                                                                                   d1pj5a3 A:220-338 N,N-dimethylglycine oxidase                                                                          d1pj5a2 A:4-219,A:339-427 N,N-dimethylglycine oxidase                                    d1pj5a4 A:428-742 N,N-dimethylglycine oxidase domain 3                                                                                                                                                                                                                                                                     d1pj5a1 A:743-830 N,N-dimethylglycine oxidase, C-terminal domain                         SCOP domains
               CATH domains 1pj5A01 A:4-85,A:145-219,A:339-421  [code=3.50.50.60, no name defined]            1pj5A02 A:86-144,A:220-338                                 1pj5A01 A:4-85,A:145-219,A:339-421  [code=3.50.50.60, no name defined]     1pj5A02 A:86-144,A:220-338 D-Amino Acid Oxidase, subunit A, domain 2                                                   1pj5A01 A:4-85,A:145-219,A:339-421  [code=3.50.50.60, no name defined]             ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1pj5A05 A:740-817 Aminomethyltransferase beta-barrel domains                  ------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhh....eeee.........hhhhh...ee.....hhhhhhhhhhhhhhhhhhee..ee.ee...eeeee.hhhhhhhhhhhhhhhhhhh...eeehhhhhhhhh...hhhhh.eeeee...eeehhhhhhhhhhhhhhhh..eee....eeeeeee..eeeeeee..eeee..eeee.hhhhhhhhhhh.......eeeeeeeeee..hhhhh............eeeehhh.eeeeee..eeeeee........hhhhh...hhhhh.......ee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee......eeee......eeeee..hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhh.eeeeee..eeeeeee.hhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhh.eeee.....eeeee..hhhhhhhhhh..........eeeeeee.....eeeeeeeeeee..eeeee..hhhhhhhhhhhhhhhhhhh......eeee....eeeeeee..hhhhhhh................eeeeee..eeeeee........eeeeeeehhhhhhhhhhhhhhhhhhh.eeehhhhhhhhhhhh...................hhhhh........hhhhhh........eeeeeeee...........eeee..eeeee...eeee....eeeeeeeee.......eeeeee..eeeeeeee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pj5 A   4 TPRIVIIGAGIVGTNLADELVTRGWNNITVLDQGPLNMPGGSTSHAPGLVFQTNPSKTMASFAKYTVEKLLSLTEDGVSCFNQVGGLEVATTETRLADLKRKLGYAAAWGIEGRLLSPAECQELYPLLDGENILGGLHVPSDGLASAARAVQLLIKRTESAGVTYRGSTTVTGIEQSGGRVTGVQTADGVIPADIVVSCAGFWGAKIGAMIGMAVPLLPLAHQYVKTTPVPAQQGRNDQPNGARLPILRHQDQDLYYREHGDRYGIGSYAHRPMPVDVDTLGAYAPETVSEHHMPSRLDFTLEDFLPAWEATKQLLPALADSEIEDGFNGIFSFTPDGGPLLGESKELDGFYVAEAVWVTHSAGVAKAMAELLTTGRSETDLGECDITRFEDVQLTPEYVSETSQQNFVEIYDVLHPLQPRLSPRNLRVSPFHARHKELGAFFLEAGGWERPYWFEANAALLKEMPAEWLPPARDAWSGMFSSPIAAAEAWKTRTAVAMYDMTPLKRLEVSGPGALKLLQELTTADLAKKPGAVTYTLLLDHAGGVRSDITVARLSEDTFQLGANGNIDTAYFERAARHQTQSGSATDWVQVRDTTGGTCCIGLWGPLARDLVSKVSDDDFTNDGLKYFRAKNVVIGGIPVTAMRLSYVGELGWELYTSADNGQRLWDALWQAGQPFGVIAAGRAAFSSLRLEKGYRSWGTDMTTEHDPFEAGLGFAVKMAKESFIGKGALEGRTEEASARRLRCLTIDDGRSIVLGKEPVFYKEQAVGYVTSAAYGYTVAKPIAYSYLPGTVSVGDSVDIEYFGRRITATVTEDPLYDPKMTRLRG 830
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773       783       793       803       813       823

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 "Pfam Domain" information available for 1PJ5)

Asymmetric Unit(hide GO term definitions)

Chain A (DMGO_ARTGO | Q9AGP8)

molecular function
	GO:0047866	dimethylglycine oxidase activity	Catalysis of the reaction: N,N-dimethylglycine + H(2)O + O(2) = formaldehyde + H(2)O(2) + sarcosine.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Asp A:818 - Pro A:819	[ RasMol ]
		Gln A:242 - Pro A:243	[ RasMol ]
		Ser A:426 - Pro A:427	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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