2JBV - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF CHOLINE OXIDASE REVEALS INSIGHTS INTO THE CATALYTIC MECHANISM

Authors :   G. T. Lountos, F. Fan, G. Gadda, A. M. Orville

Date :   13 Dec 06 (Deposition) - 25 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.86

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

Keywords :   Alcohol Oxidation, Flavoenyzme Oxidase, Covalently Linked Fad, Arthrobacter Globiformis, C4A-Adduct, Flavoprotein, Oxidoreductase, Glucose-Methanol-Choline Oxidoreductase Enzyme Superfamily (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Quaye, G. T. Lountos, F. Fan, A. M. Orville, G. Gadda
Role Of Glu312 In Binding And Positioning Of The Substrate For The Hydride Transfer Reaction In Choline Oxidase.
Biochemistry V. 47 243 2008
PubMed-ID: 18072756 | Reference-DOI: 10.1021/BI7017943
(for further references see the PDB file header)

Molecule 1 - CHOLINE OXIDASE
	Atcc	:	8010
	Chains	:	A, B
	EC Number	:	1.1.3.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Organism Scientific	:	ARTHROBACTER GLOBIFORMIS
	Organism Taxid	:	1665
	Other Details	:	COVALENT LINKAGE BETWEEN C8M ATOM OF FAO AND NE2 ATOM OF HIS99 OF CHOLINE OXIDASE

		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, 8)

No.	Name	Count	Type	Full Name
1	DMS	2	Ligand/Ion	DIMETHYL SULFOXIDE
2	FAO	2	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[(4AS,10AR)-7,8-DIMETHYL-2,4-DIOXO-1,3,4,4A,5,10A-HEXAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGENDIPHOSPHATE
3	UNX	4	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
2	FAO	1	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[(4AS,10AR)-7,8-DIMETHYL-2,4-DIOXO-1,3,4,4A,5,10A-HEXAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGENDIPHOSPHATE
3	UNX	2	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	DMS	1	Ligand/Ion	DIMETHYL SULFOXIDE
2	FAO	1	Ligand/Ion	[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[(4AS,10AR)-7,8-DIMETHYL-2,4-DIOXO-1,3,4,4A,5,10A-HEXAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGENDIPHOSPHATE
3	UNX	2	Ligand/Ion	UNKNOWN ATOM OR ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:20 , GLY A:22 , SER A:23 , ALA A:24 , GLU A:44 , ALA A:45 , TRP A:71 , ALA A:88 , ARG A:89 , ALA A:90 , LYS A:91 , VAL A:92 , GLY A:95 , CYS A:96 , SER A:97 , HIS A:99 , ASN A:100 , SER A:101 , CYS A:102 , ILE A:103 , LEU A:230 , ARG A:231 , ALA A:232 , SER A:268 , THR A:269 , GLY A:270 , ASP A:273 , VAL A:464 , TYR A:465 , HIS A:466 , ASP A:499 , ALA A:500 , ASN A:510 , PRO A:511 , ASN A:512 , VAL A:515 , DMS A:1530 , HOH A:2292 , HOH A:2450 , HOH A:2480 , HOH A:2481 , HOH A:2482 , HOH A:2483 , HOH A:2484 , UNX A:2500 , UNX A:2501	BINDING SITE FOR RESIDUE FAO A1528
2	AC2	SOFTWARE	SER A:101 , ILE A:103 , HIS A:351 , VAL A:464 , TYR A:465 , FAO A:1528 , UNX A:2500 , UNX A:2501	BINDING SITE FOR RESIDUE DMS A1530
3	AC3	SOFTWARE	GLY B:20 , GLY B:22 , SER B:23 , ALA B:24 , GLU B:44 , ALA B:45 , TRP B:71 , ALA B:88 , ARG B:89 , ALA B:90 , LYS B:91 , VAL B:92 , GLY B:95 , CYS B:96 , SER B:97 , HIS B:99 , ASN B:100 , SER B:101 , CYS B:102 , ILE B:103 , LEU B:230 , ARG B:231 , ALA B:232 , SER B:268 , THR B:269 , GLY B:270 , ASP B:273 , LEU B:277 , VAL B:464 , TYR B:465 , HIS B:466 , ASP B:499 , ALA B:500 , ASN B:510 , PRO B:511 , ASN B:512 , VAL B:515 , DMS B:1533 , HOH B:2078 , HOH B:2265 , HOH B:2451 , HOH B:2473 , HOH B:2482 , HOH B:2483 , HOH B:2484 , UNX B:2500 , UNX B:2501	BINDING SITE FOR RESIDUE FAO B1531
4	AC4	SOFTWARE	TRP B:61 , SER B:101 , ILE B:103 , TRP B:331 , HIS B:351 , VAL B:464 , FAO B:1531 , UNX B:2501	BINDING SITE FOR RESIDUE DMS B1533
5	AC5	SOFTWARE	HIS A:466 , ASN A:510 , FAO A:1528 , DMS A:1530 , UNX A:2501	BINDING SITE FOR RESIDUE UNX A2500
6	AC6	SOFTWARE	VAL A:464 , HIS A:466 , ASN A:510 , FAO A:1528 , DMS A:1530 , UNX A:2500	BINDING SITE FOR RESIDUE UNX A2501
7	AC7	SOFTWARE	HIS B:466 , ASN B:510 , FAO B:1531 , UNX B:2501	BINDING SITE FOR RESIDUE UNX B2500
8	AC8	SOFTWARE	VAL B:464 , HIS B:466 , ASN B:510 , FAO B:1531 , DMS B:1533 , UNX B:2500	BINDING SITE FOR RESIDUE UNX B2501

(no "SS Bond" information available for 2JBV)

Asymmetric Unit

No.	Residues
1	Ser A:442	-	Pro A:443
2	Ser B:442	-	Pro B:443

(no "SAP(SNP)/Variant" information available for 2JBV)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GMC_OXRED_2	PS00624	GMC oxidoreductases signature 2.	CHOX_ARTGO	270-284	2	A:270-284 B:270-284

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GMC_OXRED_2	PS00624	GMC oxidoreductases signature 2.	CHOX_ARTGO	270-284	1	A:270-284 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GMC_OXRED_2	PS00624	GMC oxidoreductases signature 2.	CHOX_ARTGO	270-284	1	- B:270-284

(no "Exon" information available for 2JBV)

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:527
 aligned with CHOX_ARTGO | Q7X2H8 from UniProtKB/Swiss-Prot  Length:546

    Alignment length:527
                                    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       390       400       410       420       430       440       450       460       470       480       490       500       510       520       
           CHOX_ARTGO     1 MHIDNIENLSDREFDYIVVGGGSAGAAVAARLSEDPAVSVALVEAGPDDRGVPEVLQLDRWMELLESGYDWDYPIEPQENGNSFMRHARAKVMGGCSSHNSCIAFWAPREDLDEWEAKYGATGWNAEAAWPLYKRLETNEDAGPDAPHHGDSGPVHLMNVPPKDPTGVALLDACEQAGIPRAKFNTGTTVVNGANFFQINRRADGTRSSSSVSYIHPIVEQENFTLLTGLRARQLVFDADRRCTGVDIVDSAFGHTHRLTARNEVVLSTGAIDTPKLLMLSGIGPAAHLAEHGIEVLVDSPGVGEHLQDHPEGVVQFEAKQPMVAESTQWWEIGIFTPTEDGLDRPDLMMHYGSVPFDMNTLRHGYPTTENGFSLTPNVTHARSRGTVRLRSRDFRDKPMVDPRYFTDPEGHDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNTVYHPVGTVRMGAVEDEMSPLDPELRVKGVTGLRVADASVMPEHVTVNPNITVMMIGERCADLIR 527
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhh...eeeeeee..hhhhhhhhhhhh......eeee........hhhhhhhhhhhhhh.......ee...........ee......hhhhhh........hhhhhhhhhhh......hhhhhhhhhhhheee...............eeeee....hhhhhhhhhhhhhh...............eeee.ee.........hhhhhhhhhhh....eeee...eeeeeee.....eeeeeee......eeeeeeeeeeee.hhhhhhhhhhhhh.eehhhhhhhh.....ee...........ee..eeeee.............eeeee..........eeeeee.......hhhhh......eeeeeeee.......eee..........eee........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhee...............................eee.hhhhh.......hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GMC_OXRED_2    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jbv A   1 MHIDNIENLSDREFDYIVVGGGSAGAAVAARLSEDPAVSVALVEAGPDDRGVPEVLQLDRWMELLESGYDWDYPIEPQENGNSFMRHARAKVMGGCSSHNSCIAFWAPREDLDEWEAKYGATGWNAEAAWPLYKRLETNEDAGPDAPHHGDSGPVHLMNVPPKDPTGVALLDACEQAGIPRAKFNTGTTVVNGANFFQINRRADGTRSSSSVSYIHPIVEQENFTLLTGLRARQLVFDADRRCTGVDIVDSAFGHTHRLTARNEVVLSTGAIDTPKLLMLSGIGPAAHLAEHGIEVLVDSPGVGEHLQDHPEGVVQFEAKQPMVAESTQWWEIGIFTPTEDGLDRPDLMMHYGSVPFDMNTLRHGYPTTENGFSLTPNVTHARSRGTVRLRSRDFRDKPMVDPRYFTDPEGHDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNTVYHPVGTVRMGAVEDEMSPLDPELRVKGVTGLRVADASVMPEHVTVNPNITVMMIGERCADLIR 527
                                    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       390       400       410       420       430       440       450       460       470       480       490       500       510       520

Chain B from PDB  Type:PROTEIN  Length:530
 aligned with CHOX_ARTGO | Q7X2H8 from UniProtKB/Swiss-Prot  Length:546

    Alignment length:530
                                    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       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530
           CHOX_ARTGO     1 MHIDNIENLSDREFDYIVVGGGSAGAAVAARLSEDPAVSVALVEAGPDDRGVPEVLQLDRWMELLESGYDWDYPIEPQENGNSFMRHARAKVMGGCSSHNSCIAFWAPREDLDEWEAKYGATGWNAEAAWPLYKRLETNEDAGPDAPHHGDSGPVHLMNVPPKDPTGVALLDACEQAGIPRAKFNTGTTVVNGANFFQINRRADGTRSSSSVSYIHPIVEQENFTLLTGLRARQLVFDADRRCTGVDIVDSAFGHTHRLTARNEVVLSTGAIDTPKLLMLSGIGPAAHLAEHGIEVLVDSPGVGEHLQDHPEGVVQFEAKQPMVAESTQWWEIGIFTPTEDGLDRPDLMMHYGSVPFDMNTLRHGYPTTENGFSLTPNVTHARSRGTVRLRSRDFRDKPMVDPRYFTDPEGHDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNTVYHPVGTVRMGAVEDEMSPLDPELRVKGVTGLRVADASVMPEHVTVNPNITVMMIGERCADLIRSAR 530
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhhhh...eeeeeee..hhhhhhhhhhhh......eeee........hhhhhhhhhhhhhh.......ee...........ee......hhhhhh........hhhhhhhhhhh......hhhhhhhhhhhheee...............eeeee....hhhhhhhhhhhhhh...............eeee.ee.........hhhhhhhhhhh....eeee...eeeeeee.....eeeeeee......eeeeeeeeeeee.hhhhhhhhhhhhh.eehhhhhhhh.....ee...........ee..eeeee.............eeeee..........eeeeee.......hhhhh......eeeeeeee.......eee..........eee........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhee...............................eee.hhhhh.......hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GMC_OXRED_2    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jbv B   1 MHIDNIENLSDREFDYIVVGGGSAGAAVAARLSEDPAVSVALVEAGPDDRGVPEVLQLDRWMELLESGYDWDYPIEPQENGNSFMRHARAKVMGGCSSHNSCIAFWAPREDLDEWEAKYGATGWNAEAAWPLYKRLETNEDAGPDAPHHGDSGPVHLMNVPPKDPTGVALLDACEQAGIPRAKFNTGTTVVNGANFFQINRRADGTRSSSSVSYIHPIVEQENFTLLTGLRARQLVFDADRRCTGVDIVDSAFGHTHRLTARNEVVLSTGAIDTPKLLMLSGIGPAAHLAEHGIEVLVDSPGVGEHLQDHPEGVVQFEAKQPMVAESTQWWEIGIFTPTEDGLDRPDLMMHYGSVPFDMNTLRHGYPTTENGFSLTPNVTHARSRGTVRLRSRDFRDKPMVDPRYFTDPEGHDMRVMVAGIRKAREIAAQPAMAEWTGRELSPGVEAQTDEELQDYIRKTHNTVYHPVGTVRMGAVEDEMSPLDPELRVKGVTGLRVADASVMPEHVTVNPNITVMMIGERCADLIRSAR 530
                                    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       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530

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 "SCOP Domain" information available for 2JBV)

(no "CATH Domain" information available for 2JBV)

(no "Pfam Domain" information available for 2JBV)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CHOX_ARTGO | Q7X2H8)

molecular function
	GO:0033713	choline:oxygen 1-oxidoreductase activity	Catalysis of the reaction: choline + O2 = betaine aldehyde + hydrogen peroxide.
	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: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.
	GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
	GO:0019285	glycine betaine biosynthetic process from choline	The chemical reactions and pathways resulting in the formation of betaine (N-trimethylglycine) from the oxidation of choline.
	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.

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	Cis Peptide Bonds
		Ser A:442 - Pro A:443	[ RasMol ]
		Ser B:442 - Pro B:443	[ RasMol ]

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	2jbv
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	CHOX_ARTGO \| Q7X2H8	:	3ljp 3nne 4mjw

(no "Related Entries Specified in the PDB File" available for 2JBV)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

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