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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CHOLESTEROL OXIDASE FROM STREPTOMYCES SP. N485D MUTANT (1.0A)

Authors :   A. Y. Lyubimov, A. Vrielink

Date :   03 Apr 09 (Deposition) - 01 Dec 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.00

Chains :   Asym./Biol. Unit : A

Keywords :   Gmc Oxidoreductase, Site-Directed Mutagenesis, Hydrophobic Tunnel, Flavoprotein, Cholesterol Metabolism, Fad, Lipid Metabolism, Oxidoreductase, Secreted, Steroid Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Y. Lyubimov, L. Chen, N. S. Sampson, A. Vrielink
A Hydrogen-Bonding Network Is Important For Oxidation And Isomerization In The Reaction Catalyzed By Cholesterol Oxidase.
Acta Crystallogr. , Sect. D V. 65 1222 2009
PubMed-ID: 19923719 | Reference-DOI: 10.1107/S0907444909037421

Molecule 1 - CHOLESTEROL OXIDASE
	Chains	:	A
	EC Number	:	1.1.3.6
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	CHOA
	Mutation	:	YES
	Organism Scientific	:	STREPTOMYCES SP.
	Organism Taxid	:	74576
	Strain	:	SA-COO
	Synonym	:	CHOD

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:16 , GLY A:17 , GLY A:19 , TYR A:20 , GLY A:21 , LEU A:39 , GLU A:40 , MET A:41 , TYR A:107 , GLY A:109 , ARG A:110 , GLY A:111 , GLY A:114 , GLY A:115 , ASN A:119 , GLY A:120 , GLY A:121 , MET A:122 , ILE A:218 , HIS A:248 , GLN A:249 , VAL A:250 , GLY A:288 , ALA A:289 , GLY A:290 , TYR A:446 , HIS A:447 , ASP A:474 , GLY A:475 , ASP A:485 , PRO A:486 , PHE A:487 , HOH A:2001 , HOH A:2006 , HOH A:2007 , HOH A:2013 , HOH A:2015 , HOH A:2019 , HOH A:2032 , HOH A:2049 , HOH A:2079 , HOH A:2088 , HOH A:2161	BINDING SITE FOR RESIDUE FAD A 510
2	AC2	SOFTWARE	GLU A:179 , GLN A:180 , LYS A:183 , ARG A:283 , HIS A:331 , TRP A:333 , ASN A:334 , HOH A:2137 , HOH A:2631	BINDING SITE FOR RESIDUE SO4 A 511

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

(no "Cis Peptide Bond" information available for 3GYI)

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GMC_OXRED_1	PS00623	GMC oxidoreductases signature 1.	CHOD_STRS0	146-169	1	A:109-132

(no "Exon" information available for 3GYI)

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:498
 aligned with CHOD_STRS0 | P12676 from UniProtKB/Swiss-Prot  Length:546

    Alignment length:498
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535        
           CHOD_STRS0    46 GYVPAVVIGTGYGAAVSALRLGEAGVQTLMLEMGQLWNQPGPDGNIFCGMLNPDKRSSWFKNRTEAPLGSFLWLDVVNRNIDPYAGVLDRVNYDQMSVYVGRGVGGGSLVNGGMAVEPKRSYFEEILPRVDSSEMYDRYFPRANSMLRVNHIDTKWFEDTEWYKFARVSREQAGKAGLGTVFVPNVYDFGYMQREAAGEVPKSALATEVIYGNNHGKQSLDKTYLAAALGTGKVTIQTLHQVKTIRQTKDGGYALTVEQKDTDGKLLATKEISCRYLFLGAGSLGSTELLVRARDTGTLPNLNSEVGAGWGPNGNIMTARANHMWNPTGAHQSSIPALGIDAWDNSDSSVFAEIAPMPAGLETWVSLYLAITKNPQRGTFVYDAATDRAKLNWTRDQNAPAVNAAKALFDRINKANGTIYRYDLFGTQLKAFADDFCYHPLGGCVLGKATDDYGRVAGYKNLYVTDGSLIPGSVGVNPFVTITALAERNVERIIKQDV 543
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3gyiA01 A:9-155,A:218-322,A:385-401,A:443-505  [code=3.50.50.60, no name defined]                                                                  3gyiA02 A:156-213,A:323-384,A:406-442                     ----3gyiA01 A:9-155,A:218-322,A:385-401,A:443-505  [code=3.50.50.60, no name defined]                        3gyiA02 A:156-213,A:323-384,A:406-442                         3gyiA01          ----3gyiA02 A:156-213,A:323-384,A:406-4423gyiA01 A:9-155,A:218-322,A:385-401,A:443-505                  - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..hhhhhhhhhhhhhh...eeeee.....................hhhhh...........hhhhhhhhh.........eeeeee..eeeeee...hhhhhh........hhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhh..hhhhhhhhhhhhhh...eee.....hhhhhhhhhh.....hhhhh...............hhhhhhhhh..eeeee.eeeeeeee.....eeeeeeee.....eeeeeeeee.eeee.hhhhhhhhhhhhhhhh...................eeeeee................eeeee.......eeeeee.........eeeeeeee.......eeee....eeee..hhhhhhhhhhhhhhhhhhhhhhhh.ee...........ee..ee........................eee.hhhhh.......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------GMC_OXRED_1             -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gyi A   9 GYVPAVVIGTGYGAAVSALRLGEAGVQTLMLEMGQLWNQPGPDGNIFCGMLNPDKRSSWFKNRTEAPLGSFLWLDVVNRNIDPYAGVLDRVNYDQMSVYVGRGVGGGSLVNGGMAVEPKRSYFEEILPRVDSSEMYDRYFPRANSMLRVNHIDTKWFEDTEWYKFARVSREQAGKAGLGTVFVPNVYDFGYMQREAAGEVPKSALATEVIYGNNHGKQSLDKTYLAAALGTGKVTIQTLHQVKTIRQTKDGGYALTVEQKDTDGKLLATKEISCRYLFLGAGSLGSTELLVRARDTGTLPNLNSEVGAGWGPNGNIMTARANHMWNPTGAHQSSIPALGIDAWDNSDSSVFAEIAPMPAGLETWVSLYLAITKNPQRGTFVYDAATDRAKLNWTRDQNAPAVNAAKALFDRINKANGTIYRYDLFGTQLKAFADDFCYHPLGGCVLGKATDDYGRVAGYKNLYVTDGSLIPGSVGVDPFVTITALAERNVERIIKQDV 506
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498

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 3GYI)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Cholesterol Oxidase; domain 2 (20)

Homologous Superfamily: Cholesterol Oxidase; domain 2 (20)

Sa-coo (Streptomyces sp) (9)

3gyiA02

A:156-213,A:323-384,A:406-442

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

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

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

Sa-coo (Streptomyces sp) (9)

3gyiA01

A:9-155,A:218-322,A:385-401,A:443-505

(no "Pfam Domain" information available for 3GYI)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CHOD_STRS0 | P12676)

molecular function
	GO:0016995	cholesterol oxidase activity	Catalysis of the reaction: cholesterol + O2 = cholest-5-en-3-one + H2O2.
	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:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	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.
	GO:0004769	steroid delta-isomerase activity	Catalysis of the reaction: a 3-oxo-delta(5)-steroid = a 3-oxo-delta(4)-steroid.
biological process
	GO:0008203	cholesterol metabolic process	The chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones. It is a component of the plasma membrane lipid bilayer and of plasma lipoproteins and can be found in all animal tissues.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	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:0008202	steroid metabolic process	The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric/Biological Unit
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1ijh	1.5A STRUCTURE OF N485L MUTANT OF CHOLESTEROL OXIDASE
1mxt	ATOMIC RESOLUTION STRUCTURE OF WT CHOLESTEROL OXIDASE
3gyj

Description

Compounds

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Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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