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Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   L-ASPARTATE OXIDASE: R386L MUTANT

Authors :   R. T. Bossi, A. Mattevi

Date :   19 Dec 01 (Deposition) - 17 Apr 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Succinate Dehydrogenase, Fumarate Reductase Family Of Oxidoreductases (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. T. Bossi, A. Negri, G. Tedeschi, A. Mattevi
Structure Of Fad-Bound L-Aspartate Oxidase: Insight Into Substrate Specificity And Catalysis.
Biochemistry V. 41 3018 2002
PubMed-ID: 11863440 | Reference-DOI: 10.1021/BI015939R
(for further references see the PDB file header)

Molecule 1 - L-ASPARTATE OXIDASE
	Chains	:	A
	EC Number	:	1.4.3.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Gene	:	NADB
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:244 , THR A:259 , GLU A:260	BINDING SITE FOR RESIDUE CL A 541
2	AC2	SOFTWARE	THR A:353 , GLY A:355 , GLU A:375 , SER A:377	BINDING SITE FOR RESIDUE NA A 542
3	AC3	SOFTWARE	ILE A:14 , GLY A:15 , SER A:16 , ALA A:18 , ALA A:19 , LYS A:38 , GLY A:44 , SER A:45 , THR A:46 , TYR A:48 , ALA A:49 , GLN A:50 , GLY A:51 , GLY A:52 , THR A:160 , ASN A:161 , ALA A:162 , ALA A:203 , THR A:204 , GLY A:205 , ASN A:216 , ILE A:219 , ASP A:223 , LEU A:257 , HIS A:351 , TYR A:352 , GLY A:374 , GLU A:375 , SER A:389 , SER A:391 , LEU A:392	BINDING SITE FOR RESIDUE FAD A 800

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

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

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

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

(no "Exon" information available for 1KNR)

Asymmetric/Biological 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:529
 aligned with NADB_ECOLI | P10902 from UniProtKB/Swiss-Prot  Length:540

    Alignment length:529
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524         
           NADB_ECOLI     5 PEHSCDVLIIGSGAAGLSLALRLADQHQVIVLSKGPVTEGSTFYAQGGIAAVFDETDSIDSHVEDTLIAGAGICDRHAVEFVASNARSCVQWLIDQGVLFDTHIQPNGEESYHLTREGGHSHRRILHAADATGREVETTLVSKALNHPNIRVLERSNAVDLIVSDKIGLPGTRRVVGAWVWNRNKETVETCHAKAVVLATGGASKVYQYTTNPDISSGDGIAMAWRAGCRVANLEFNQFHPTALYHPQARNFLLTEALRGEGAYLKRPDGTRFMPDFDERGELAPRDIVARAIDHEMKRLGADCMFLDISHKPADFIRQHFPMIYEKLLGLGIDLTQEPVPIVPAAHYTCGGVMVDDHGRTDVEGLYAIGEVSYTGLHGANRMASNSLLECLVYGWSAAEDITRRMPYAHDISTLPPWDESRVENPDERVVIQHNWHELRLFMWDYVGIVRTTKRLERALRRITMLQQEIDEYYAHFRVSNNLLELRNLVQVAELIVRCAMMRKESRGLHFTLDYPELLTHSGPSILSP 533
               SCOP domains d1knra2 A:5-237,A:354-422 L-aspartate oxidase                                                                                                                                                                                            d1knra3 A:238-353 L-aspartate oxidase                                                                               d1knra2 A:5-237,A:354-422 L-aspartate oxidase                        d1knra1 A:423-533 L-aspartate oxidase                                                                           SCOP domains
               CATH domains 1knrA01 A:5-244,A:349-424  [code=3.50.50.60, no name defined]                                                                                                                                                                                   1knrA02 A:245-348 Flavocytochrome C3; Chain A, domain 1                                                 1knrA01 A:5-244,A:349-424  [code=3.50.50.60, no name defined]               1knrA03 A:425-533  [code=1.20.58.100, no name defined]                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..eeee..hhhhhhhhhhhhh...eeee.......hhhhhh...ee.......hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..................ee.........ee....hhhhhhhhhhhhhhhh...eeee..eeeeeeee.hhh.......eeeeeeee.hhh.eeeee..eeee....hhhhh..........hhhhhhhhhh...ee....eeeeeeee..........hhhhhhh..eee......hhhhh..hhhhhhhhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhh.........eeeeeeeeee..eee...........eee....ee...........hhhhhhhhhhhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh......................ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1knr A   5 PEHSCDVLIIGSGAAGLSLALRLADQHQVIVLSKGPVTEGSTFYAQGGIAAVFDETDSIDSHVEDTLIAGAGICDRHAVEFVASNARSCVQWLIDQGVLFDTHIQPNGEESYHLTREGGHSHRRILHAADATGREVETTLVSKALNHPNIRVLERTNAVDLIVSDKIGLPGTRRVVGAWVWNRNKETVETCHAKAVVLATGGASKVYQYTTNPDISSGDGIAMAWRAGCRVANLEFNQFHPTALYHPQARNFLLTEALRGEGAYLKRPDGTRFMPDFDERGELAPRDIVARAIDHEMKRLGADCMFLDISHKPADFIRQHFPMIYEKLLGLGIDLTQEPVPIVPAAHYTCGGVMVDDHGRTDVEGLYAIGEVSYTGLHGANLMASNSLLECLVYGWSAAEDITRRMPYAHDISTLPPWDESRVENPDERVVIQHNWHELRLFMWDYVGIVRTTKRLERALRRITMLQQEIDEYYAHFRVSNNLLELRNLVQVAELIVRCAMMRKESRGLHFTLDYPELLTHSGPSILSP 533
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524

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 1KNR)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NADB_ECOLI | P10902)

molecular function
	GO:0008734	L-aspartate oxidase activity	Catalysis of the reaction: L-aspartate + O2 = iminosuccinate + hydrogen peroxide.
	GO:0044318	L-aspartate:fumarate oxidoreductase activity	Catalysis of the reaction: L-aspartate + fumarate = alpha-iminosuccinate + succinate.
	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: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:0034628	'de novo' NAD biosynthetic process from aspartate	The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD), beginning with the synthesis of aspartate from simpler precursors; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
	GO:0009435	NAD biosynthetic process	The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide, a coenzyme present in most living cells and derived from the B vitamin nicotinic acid; biosynthesis may be of either the oxidized form, NAD, or the reduced form, NADH.
	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:0019363	pyridine nucleotide biosynthetic process	The chemical reactions and pathways resulting in the formation of a pyridine nucleotide, a nucleotide characterized by a pyridine derivative as a nitrogen base.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1knr)

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	1.4.3.16
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	NADB_ECOLI \| P10902	:	1chu 1knp

1chu	1CHU CONTAINS L-ASPARTATE OXIDASE: WILD TYPE APOFORM
1knp	1KNP CONTAINS L-ASPARTATE OXIDASE: R386L MUTANT HOLOFORM IN COMPLEX WITH SUCCINATE

Description

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Ligands, Modified Residues, Ions (3, 3)

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