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Title :   CRYSTAL STRUCTURE OF A FULLY FUNCTIONAL LACCASE FROM THE LIGNINOLYTIC FUNGUS PYCNOPORUS CINNABARINUS

Authors :   K. Piontek, T. Choinowski, M. Antorini, I. Herpoel-Gimbert, D. A. Plat J. C. Sigoillot, M. Asther, K. Winterhalter

Date :   17 Nov 10 (Deposition) - 30 Nov 11 (Release) - 30 Nov 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

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

Keywords :   Blue Multi-Copper Oxidase, Phenol Oxidase, Lignin Degradation, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Piontek, T. Choinowski, M. Antorini, I. Herpoel-Gimbert, M. Asther, D. A. Plattner
Substrate Binding And Copper Geometry In Laccases
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - LACCASE
	Chains	:	A
	EC Number	:	1.10.3.2
	Fragment	:	RESIDUES 22-518
	Organism Scientific	:	PYCNOPORUS CINNABARINUS
	Organism Taxid	:	5643
	Other Details	:	THIS ORGANISM IS ALSO KNOWN AS CINNABAR-RED POLYPORE
	Strain	:	SS3

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (11, 34)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	AS8	1	Ligand/Ion	ACETYLSULFATE
3	BMA	2	Ligand/Ion	BETA-D-MANNOSE
4	CU	4	Ligand/Ion	COPPER (II) ION
5	GOL	4	Ligand/Ion	GLYCEROL
6	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
7	NA	1	Ligand/Ion	SODIUM ION
8	NAG	9	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
9	PER	1	Ligand/Ion	PEROXIDE ION
10	SO4	2	Ligand/Ion	SULFATE ION
11	ZN	8	Ligand/Ion	ZINC ION

Biological Unit 1 (8, 42)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	AS8	2	Ligand/Ion	ACETYLSULFATE
3	BMA	4	Ligand/Ion	BETA-D-MANNOSE
4	CU	-1	Ligand/Ion	COPPER (II) ION
5	GOL	8	Ligand/Ion	GLYCEROL
6	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
7	NA	-1	Ligand/Ion	SODIUM ION
8	NAG	18	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
9	PER	2	Ligand/Ion	PEROXIDE ION
10	SO4	4	Ligand/Ion	SULFATE ION
11	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:395 , CYS A:451 , ILE A:453 , HIS A:456	BINDING SITE FOR RESIDUE CU A 501
02	AC2	SOFTWARE	HIS A:111 , HIS A:398 , HIS A:400 , HIS A:450 , PER A:505	BINDING SITE FOR RESIDUE CU A 502
03	AC3	SOFTWARE	HIS A:66 , HIS A:109 , HIS A:452 , PER A:505	BINDING SITE FOR RESIDUE CU A 503
04	AC4	SOFTWARE	HIS A:64 , HIS A:66 , HIS A:398 , HIS A:400 , PER A:505 , HOH A:2142	BINDING SITE FOR RESIDUE CU A 504
05	AC5	SOFTWARE	HIS A:64 , HIS A:66 , HIS A:109 , HIS A:111 , HIS A:398 , HIS A:400 , HIS A:450 , HIS A:452 , CU A:502 , CU A:503 , CU A:504 , HOH A:2657	BINDING SITE FOR RESIDUE PER A 505
06	AC6	SOFTWARE	ASN A:377	BINDING SITE FOR RESIDUE NAG A 550
07	AC7	SOFTWARE	PRO A:163 , ASP A:206 , GLY A:392 , HIS A:456 , HOH A:2675 , HOH A:2676 , HOH A:2677	BINDING SITE FOR RESIDUE AS8 A 601
08	AC8	SOFTWARE	PHE A:69 , HIS A:402 , ALA A:403 , ASN A:442 , ZN A:710 , HOH A:2686 , HOH A:2687	BINDING SITE FOR RESIDUE ACT A 602
09	AC9	SOFTWARE	LEU A:174 , ASP A:184 , ARG A:195 , ASP A:249 , HOH A:2679	BINDING SITE FOR RESIDUE SO4 A 603
10	BC1	SOFTWARE	SER A:376 , ASP A:468 , ASP A:471 , ZN A:712 , HOH A:2680	BINDING SITE FOR RESIDUE SO4 A 604
11	BC2	SOFTWARE	ALA A:80 , HIS A:111 , SER A:113 , PRO A:346 , LEU A:457 , HOH A:2604 , HOH A:2606 , HOH A:2681 , HOH A:2682	BINDING SITE FOR RESIDUE GOL A 610
12	BC3	SOFTWARE	ILE A:213 , HIS A:216 , ASP A:234 , THR A:294 , HOH A:2373 , HOH A:2458 , HOH A:2683 , HOH A:2684	BINDING SITE FOR RESIDUE GOL A 611
13	BC4	SOFTWARE	HIS A:216 , THR A:217 , ASP A:249 , SER A:251 , GLN A:252 , HOH A:2685	BINDING SITE FOR RESIDUE GOL A 612
14	BC5	SOFTWARE	ASP A:128 , PRO A:129 , ASP A:131 , ALA A:134 , TYR A:137 , ASP A:140 , HOH A:2256	BINDING SITE FOR RESIDUE GOL A 613
15	BC6	SOFTWARE	HIS A:402 , ASN A:442 , ACT A:602 , HOH A:2686 , HOH A:2687	BINDING SITE FOR RESIDUE ZN A 710
16	BC7	SOFTWARE	GLU A:23 , ASP A:282 , HOH A:2688 , HOH A:2689 , HOH A:2690 , HOH A:2691	BINDING SITE FOR RESIDUE ZN A 711
17	BC8	SOFTWARE	ASP A:468 , ASP A:471 , SO4 A:604 , HOH A:2692	BINDING SITE FOR RESIDUE ZN A 712
18	BC9	SOFTWARE	HIS A:342 , GLU A:368 , HOH A:2693 , HOH A:2694 , HOH A:2695	BINDING SITE FOR RESIDUE ZN A 713
19	CC1	SOFTWARE	HIS A:306 , HOH A:2483 , HOH A:2696 , HOH A:2697 , HOH A:2698 , HOH A:2699	BINDING SITE FOR RESIDUE ZN A 714
20	CC2	SOFTWARE	HIS A:91 , HOH A:2700 , HOH A:2701 , HOH A:2702 , HOH A:2703 , HOH A:2704	BINDING SITE FOR RESIDUE ZN A 715
21	CC3	SOFTWARE	HIS A:55 , HOH A:2705 , HOH A:2706 , HOH A:2707 , HOH A:2708	BINDING SITE FOR RESIDUE ZN A 716
22	CC4	SOFTWARE	ASP A:418 , HOH A:2709 , HOH A:2710 , HOH A:2712	BINDING SITE FOR RESIDUE ZN A 717
23	CC5	SOFTWARE	GLY A:266 , ASN A:331 , ASN A:389 , HOH A:2509 , HOH A:2510	BINDING SITE FOR RESIDUE NA A 718
24	CC6	SOFTWARE	ARG A:22 , GLU A:23 , ASN A:54 , MET A:57 , HIS A:153 , VAL A:154 , ALA A:155 , LEU A:158 , HOH A:2658 , HOH A:2659 , HOH A:2660 , HOH A:2661 , HOH A:2663 , HOH A:2664 , HOH A:2691	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 54 RESIDUES 510 TO 513
25	CC7	SOFTWARE	ASN A:215 , SER A:291 , VAL A:292 , THR A:294	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 215 RESIDUES 530 TO 531
26	CC8	SOFTWARE	ASN A:333 , THR A:335 , ASN A:336 , PHE A:338	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 333 RESIDUES 540 TO 541
27	CC9	SOFTWARE	ASN A:327 , SER A:383 , ASN A:434 , HOH A:2572 , HOH A:2667 , HOH A:2668 , HOH A:2670 , HOH A:2671 , HOH A:2672 , HOH A:2673 , HOH A:2674	BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 434 RESIDUES 560 TO 562

Asymmetric Unit

No.	Residues
1	A:85	-	A:486
2	A:117	-	A:205

Asymmetric Unit

No.	Residues
1	Gly A:3	-	Pro A:4
2	Thr A:31	-	Pro A:32
3	Val A:366	-	Pro A:367
4	Phe A:393	-	Pro A:394

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

(no "PROSITE Motif" information available for 2XYB)

(no "Exon" information available for 2XYB)

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:497
 aligned with Q9UVQ2_PYCCI | Q9UVQ2 from UniProtKB/TrEMBL  Length:518

    Alignment length:497
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       
         Q9UVQ2_PYCCI    22 AIGPVADLTLTNAQVSPDGFAREAVVVNGITPAPLITGNKGDRFQLNVIDQLTNHTMLKTSSIHWHGFFQQGTNWADGPAFVNQCPIASGHSFLYDFQVPDQAGTFWYHSHLSTQYCDGLRGPFVVYDPNDPHASLYDIDNDDTVITLADWYHVAAKLGPRFPFGSDSTLINGLGRTTGIAPSDLAVIKVTQGKRYRFRLVSLSCDPNHTFSIDNHTMTIIEADSINTQPLEVDSIQIFAAQRYSFVLDASQPVDNYWIRANPAFGNTGFAGGINSAILRYDGAPEIEPTSVQTTPTKPLNEVDLHPLSPMPVPGSPEPGGVDKPLNLVFNFNGTNFFINDHTFVPPSVPVLLQILSGAQAAQDLVPEGSVFVLPSNSSIEISFPATANAPGFPHPFHLHGHAFAVVRSAGSSVYNYDNPIFRDVVSTGQPGDNVTIRFETNNPGPWFLHCHIDFHLDAGFAVVMAEDTPDTKAANPVPQAWSDLCPIYDALDPSDL 518
               SCOP domains d2xyba1 A:1-130 automated matches                                                                                                 d2xyba2 A:131-300 automated matches                                                                                                                                       d2xyba3 A:301-497 automated matches                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee......eeeeee........eeee...eeeeeeee...hhhhh....eeee......hhhhh..............eeeeeee.....eeeeeee...hhhhhh.eeeeeee.....hhhhh...hhh.eeeeeee................eeee...............eeee....eeeeeeee......eeeee....eeeeee..eeeeeeee..eee....eeeeeee......eeeeeeee......hhhhh.eeeeee...................hhhhh..................eeee..eee....eee..........hhhhhhhh...hhhhh.....eeee....eeeeeee..........eeee....eeeee.............ee.eee......eeeeeee....eeeeeee.hhhhhhh..eeeeee...hhhhhh..hhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xyb A   1 AIGPVADLTLTNAQVSPDGFAREAVVVNGITPAPLITGNKGDRFQLNVIDQLTNHTMLKTSSIHWHGFFQQGTNWADGPAFVNQCPIASGHSFLYDFQVPDQAGTFWYHSHLSTQYCDGLRGPFVVYDPNDPHASLYDIDNDDTVITLADWYHVAAKLGPRFPFGSDSTLINGLGRTTGIAPSDLAVIKVTQGKRYRFRLVSLSCDPNHTFSIDNHTMTIIEADSINTQPLEVDSIQIFAAQRYSFVLDASQPVDNYWIRANPAFGNTGFAGGINSAILRYDGAPEIEPTSVQTTPTKPLNEVDLHPLSPMPVPGSPEPGGVDKPLNLVFNFNGTNFFINDHTFVPPSVPVLLQILSGAQAAQDLVPEGSVFVLPSNSSIEISFPATANAPGFPHPFHLHGHAFAVVRSAGSSVYNYDNPIFRDVVSTGQPGDNVTIRFETNNPGPWFLHCHIDFHLDAGFAVVMAEDTPDTKAANPVPQAWSDLCPIYDALDPSDL 497
                                    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

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: automated matches (57)

Protein domain: automated matches (57)

Pycnoporus cinnabarinus [TaxId: 5643] (1)

1a	d2xyba1	A:1-130
1b	d2xyba2	A:131-300
1c	d2xyba3	A:301-497

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (Q9UVQ2_PYCCI | Q9UVQ2)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0052716	hydroquinone:oxygen oxidoreductase activity	Catalysis of the reaction: 4 hydroquinone + O2 = 4 benzosemiquinone + 4 H2O.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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
		Gly A:3 - Pro A:4	[ RasMol ]
		Phe A:393 - Pro A:394	[ RasMol ]
		Thr A:31 - Pro A:32	[ RasMol ]
		Val A:366 - Pro A:367	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (11, 34)

Sites (27, 27)

SS Bonds (2, 2)

Cis Peptide Bonds (4, 4)

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