3LSM - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   PYRANOSE 2-OXIDASE H167A MUTANT WITH FLAVIN N(5) SULFITE ADDUCT

Authors :   T. C. Tan, O. Spadiut, C. Divne

Date :   12 Feb 10 (Deposition) - 25 Aug 10 (Release) - 24 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Oxidoreductase, Gmc Oxidoreductase, H167A Mutant, Rossmann Fold, Phbh Fold, Homotetramer, Covalently Linked Fad, Flavin N(5)-Sulfite Adduct (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. C. Tan, W. Pitsawong, T. Wongnate, O. Spadiut, D. Haltrich, P. Chaiyen, C. Divne
H-Bonding And Positive Charge At The N5/O4 Locus Are Critical For Covalent Flavin Attachment In Trametes Pyranos 2-Oxidase.
J. Mol. Biol. V. 402 578 2010
PubMed-ID: 20708626 | Reference-DOI: 10.1016/J.JMB.2010.08.011

Molecule 1 - PYRANOSE 2-OXIDASE
	Chains	:	A, B
	EC Number	:	1.1.3.10
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21(D+)
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	P2O
	Mutation	:	YES
	Organism Common	:	WHITE-ROT FUNGUS
	Organism Scientific	:	TRAMETES OCHRACEA
	Organism Taxid	:	230624
	Synonym	:	PYRANOSE OXIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 9)

No.	Name	Count	Type	Full Name
1	12P	2	Ligand/Ion	DODECAETHYLENE GLYCOL
2	GLC	1	Ligand/Ion	ALPHA-D-GLUCOSE
3	SFD	2	Ligand/Ion	(S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHOXY)(HYDROXY)PHOSPHORYLOXY)(HYDROXY)PHOSPHORYLOXY)-2,3,4-TRIHYDROXYPENTYL)-7,8-DIMETHYL-2,4-DIOXO-2,3,4,4A-TETRAHYDROBENZO[G]PTERIDINE-5(10H)-SULFONIC ACID
4	SO3	4	Ligand/Ion	SULFITE ION

Biological Unit 1 (4, 18)

No.	Name	Count	Type	Full Name
1	12P	4	Ligand/Ion	DODECAETHYLENE GLYCOL
2	GLC	2	Ligand/Ion	ALPHA-D-GLUCOSE
3	SFD	4	Ligand/Ion	(S)-10-((2S,3S,4R)-5-((S)-((S)-(((2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXY-TETRAHYDROFURAN-2-YL)METHOXY)(HYDROXY)PHOSPHORYLOXY)(HYDROXY)PHOSPHORYLOXY)-2,3,4-TRIHYDROXYPENTYL)-7,8-DIMETHYL-2,4-DIOXO-2,3,4,4A-TETRAHYDROBENZO[G]PTERIDINE-5(10H)-SULFONIC ACID
4	SO3	8	Ligand/Ion	SULFITE ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:53 , GLY A:55 , PRO A:56 , ILE A:57 , ASP A:76 , ILE A:77 , THR A:158 , ARG A:159 , VAL A:160 , GLY A:163 , MET A:164 , ALA A:167 , TRP A:168 , THR A:169 , CYS A:170 , ALA A:171 , VAL A:281 , CYS A:283 , THR A:319 , ALA A:320 , HIS A:324 , ARG A:472 , VAL A:546 , LEU A:547 , HIS A:548 , ASN A:593 , THR A:595 , HOH A:1001 , HOH A:1024 , HOH A:1057 , HOH A:1095 , HOH A:1103 , HOH A:1132 , HOH A:1136 , HOH A:1137 , HOH A:1171 , HOH A:1637	BINDING SITE FOR RESIDUE SFD A 801
2	AC2	SOFTWARE	ARG A:571 , GLY A:574 , HOH A:1992	BINDING SITE FOR RESIDUE SO3 A 910
3	AC3	SOFTWARE	LYS A:576 , HOH A:1459 , HOH A:1503 , HOH A:1992 , LYS B:403 , HIS B:404 , PRO B:405	BINDING SITE FOR RESIDUE SO3 A 911
4	AC4	SOFTWARE	ARG A:63 , GLU A:64 , GLY A:67 , LYS A:201 , TYR A:205 , LYS A:610 , HOH A:2002	BINDING SITE FOR RESIDUE GLC A 912
5	AC5	SOFTWARE	SER A:134 , PRO A:144 , GLN A:146 , PRO A:148 , HOH A:1814	BINDING SITE FOR RESIDUE 12P A 901
6	AC6	SOFTWARE	VAL B:52 , GLY B:53 , GLY B:55 , PRO B:56 , ILE B:57 , ASP B:76 , ILE B:77 , THR B:158 , ARG B:159 , VAL B:160 , GLY B:163 , MET B:164 , ALA B:167 , TRP B:168 , THR B:169 , CYS B:170 , ALA B:171 , VAL B:281 , CYS B:283 , THR B:319 , ALA B:320 , HIS B:324 , ARG B:472 , VAL B:546 , LEU B:547 , HIS B:548 , ASN B:593 , THR B:595 , HOH B:1018 , HOH B:1019 , HOH B:1034 , HOH B:1104 , HOH B:1110 , HOH B:1122 , HOH B:1172 , HOH B:1475 , HOH B:1911	BINDING SITE FOR RESIDUE SFD B 801
7	AC7	SOFTWARE	SER A:400 , ARG B:571 , GLY B:574 , LYS B:576 , HOH B:2150	BINDING SITE FOR RESIDUE SO3 B 910
8	AC8	SOFTWARE	HIS B:415 , HIS B:419 , PRO B:427 , PHE B:428	BINDING SITE FOR RESIDUE SO3 B 911
9	AC9	SOFTWARE	SER B:134 , PRO B:144 , GLU B:145 , GLN B:146 , ASP B:147 , PRO B:148 , HOH B:1682 , HOH B:2029 , HOH B:2077	BINDING SITE FOR RESIDUE 12P B 902

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

Asymmetric Unit

No.	Residues
1	Arg A:265	-	Pro A:266
2	Arg B:265	-	Pro B:266

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

(no "PROSITE Motif" information available for 3LSM)

(no "Exon" information available for 3LSM)

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:574
 aligned with Q7ZA32_TRAOC | Q7ZA32 from UniProtKB/TrEMBL  Length:623

    Alignment length:574
                                    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       534       544       554       564       574       584       594       604       614    
         Q7ZA32_TRAOC    45 IKYDVVIVGSGPIGCTYARELVGAGYKVAMFDIGEIDSGLKIGAHKKNTVEYQKNIDKFVNVIQGQLMSVSVPVNTLVVDTLSPTSWQASTFFVRNGSNPEQDPLRNLSGQAVTRVVGGMSTHWTCATPRFDREQRPLLVKDDADADDAEWDRLYTKAESYFQTGTDQFKESIRHNLVLNKLTEEYKGQRDFQQIPLAATRRSPTFVEWSSANTVFDLQNRPNTDAPEERFNLFPAVACERVVRNALNSEIESLHIHDLISGDRFEIKADVYVLTAGAVHNTQLLVNSGFGQLGRPNPANPPELLPSLGSYITEQSLVFCQTVMSTELIDSVKSDMTIRGTPGELTYSVTYTPGASTNKHPDWWNEKVKNHMMQHQEDPLPIPFEDPEPQVTTLFQPSHPWHTQIHRDAFSYGAVQQSIDSRLIVDWRFFGRTEPKEENKLWFSDKITDAYNMPQPTFDFRFPAGRTSKEAEDMMTDMCVMSAKIGGFLPGSLPQFMEPGLVLHLGGTHRMGFDEKEDNCCVNTDSRVFGFKNLFLGGCGNIPTAYGANPTLTAMSLAIKSCEYIKQNFTPSPF 618
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhhhhh.ee.................................hhhhh....ee....hhhhhh........hhhhh......hhhhhhhhhhhhhhhhhhhhhee......hhhhhhhhhhhhhhhh.....ee..eeeeeee..eeee.hhhhhh....eee..eeeeeeeee..eeeeeeee......eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh............................eeeeeeeehhhhhhhhh...eee........eee..........hhhhhhhhhhhhhhh..............eee........eeeeee.............hhh.eeeeeeee........eeeeeeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhh..eee......ee.....................................eee.hhhhh.......hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lsm A  45 IKYDVVIVGSGPIGCTYARELVGAGYKVAMFDIGEIDSGLKIGAHKKNTVEYQKNIDKFVNVIQGQLMSVSVPVNTLVVDTLSPTSWQASTFFVRNGSNPEQDPLRNLSGQAVTRVVGGMSTAWTCATPRFDREQRPLLVKDDADADDAEWDRLYTKAESYFQTGTDQFKESIRHNLVLNKLTEEYKGQRDFQQIPLAATRRSPTFVEWSSANTVFDLQNRPNTDAPEERFNLFPAVACERVVRNALNSEIESLHIHDLISGDRFEIKADVYVLTAGAVHNTQLLVNSGFGQLGRPNPANPPELLPSLGSYITEQSLVFCQTVMSTELIDSVKSDMTIRGTPGELTYSVTYTPGASTNKHPDWWNEKVKNHMMQHQEDPLPIPFEDPEPQVTTLFQPSHPWHTQIHRDAFSYGAVQQSIDSRLIVDWRFFGRTEPKEENKLWFSDKITDAYNMPQPTFDFRFPAGRTSKEAEDMMTDMCVMSAKIGGFLPGSLPQFMEPGLVLHLGGTHRMGFDEKEDNCCVNTDSRVFGFKNLFLGGCGNIPTAYGANPTLTAMSLAIKSCEYIKQNFTPSPF 618
                                    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       534       544       554       564       574       584       594       604       614

Chain B from PDB  Type:PROTEIN  Length:576
 aligned with Q7ZA32_TRAOC | Q7ZA32 from UniProtKB/TrEMBL  Length:623

    Alignment length:576
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612      
         Q7ZA32_TRAOC    43 MDIKYDVVIVGSGPIGCTYARELVGAGYKVAMFDIGEIDSGLKIGAHKKNTVEYQKNIDKFVNVIQGQLMSVSVPVNTLVVDTLSPTSWQASTFFVRNGSNPEQDPLRNLSGQAVTRVVGGMSTHWTCATPRFDREQRPLLVKDDADADDAEWDRLYTKAESYFQTGTDQFKESIRHNLVLNKLTEEYKGQRDFQQIPLAATRRSPTFVEWSSANTVFDLQNRPNTDAPEERFNLFPAVACERVVRNALNSEIESLHIHDLISGDRFEIKADVYVLTAGAVHNTQLLVNSGFGQLGRPNPANPPELLPSLGSYITEQSLVFCQTVMSTELIDSVKSDMTIRGTPGELTYSVTYTPGASTNKHPDWWNEKVKNHMMQHQEDPLPIPFEDPEPQVTTLFQPSHPWHTQIHRDAFSYGAVQQSIDSRLIVDWRFFGRTEPKEENKLWFSDKITDAYNMPQPTFDFRFPAGRTSKEAEDMMTDMCVMSAKIGGFLPGSLPQFMEPGLVLHLGGTHRMGFDEKEDNCCVNTDSRVFGFKNLFLGGCGNIPTAYGANPTLTAMSLAIKSCEYIKQNFTPSPF 618
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GMC_oxred_C-3lsmB01 B:540-605                                     ------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GMC_oxred_C-3lsmB02 B:540-605                                     ------------- Pfam domains (2)
         Sec.struct. author ...eeeeeee..hhhhhhhhhhhhhh..eeeee.................hhhhhhh..hhhhhhhhh.ee..........................................ee....hhhhhh........hhhhh......hhhhhhhhhhhhhhhhhhhhhee......hhhhhhhhhhhhhhh......ee..eeeeeee..eeee.hhhhhh....eee..eeeeeeeee..eeeeeeee......eeeeeeee.....eeeeeeeeeee..hhhhhhhhhhhh............................eeeeeeeehhhhhhhhh...eee........eee..........hhhhhhhhhhhhhhh..............eee........eeeeee.............hhh.eeeeeeee........eeeeeeeee.....eeeeee.....hhhhhhhhhhhhhhhhhhh..eee......ee.....................................eee.hhhhh.......hhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lsm B  43 MDIKYDVVIVGSGPIGCTYARELVGAGYKVAMFDIGEIDSGLKIGAHKKNTVEYQKNIDKFVNVIQGQLMSVSVPVNTLVVDTLSPTSWQASTFFVRNGSNPEQDPLRNLSGQAVTRVVGGMSTAWTCATPRFDREQRPLLVKDDADADDAEWDRLYTKAESYFQTGTDQFKESIRHNLVLNKLTEEYKGQRDFQQIPLAATRRSPTFVEWSSANTVFDLQNRPNTDAPEERFNLFPAVACERVVRNALNSEIESLHIHDLISGDRFEIKADVYVLTAGAVHNTQLLVNSGFGQLGRPNPANPPELLPSLGSYITEQSLVFCQTVMSTELIDSVKSDMTIRGTPGELTYSVTYTPGASTNKHPDWWNEKVKNHMMQHQEDPLPIPFEDPEPQVTTLFQPSHPWHTQIHRDAFSYGAVQQSIDSRLIVDWRFFGRTEPKEENKLWFSDKITDAYNMPQPTFDFRFPAGRTSKEAEDMMTDMCVMSAKIGGFLPGSLPQFMEPGLVLHLGGTHRMGFDEKEDNCCVNTDSRVFGFKNLFLGGCGNIPTAYGANPTLTAMSLAIKSCEYIKQNFTPSPF 618
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612

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 3LSM)

(no "CATH Domain" information available for 3LSM)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: GMC_oxred_C] (22)

Family: GMC_oxred_C (22)

Trametes ochracea (White-rot fungus) (Trametes multicolor) (13)

1a	GMC_oxred_C-3lsmB01	B:540-605
1b	GMC_oxred_C-3lsmB02	B:540-605

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q7ZA32_TRAOC | Q7ZA32)

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: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.
	GO:0050233	pyranose oxidase activity	Catalysis of the reaction: D-glucose + O(2) = 2-dehydro-D-glucose + H(2)O(2).
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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	Ligands, Modified Residues, Ions
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		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:265 - Pro A:266	[ RasMol ]
		Arg B:265 - Pro B:266	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3lsm
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 9)

Sites (9, 9)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (6, 6)

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