1W7C - JenaLib

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Title :   PPLO AT 1.23 ANGSTROMS

Authors :   A. P. Duff, A. E. Cohen, P. J. Ellis, J. M. Guss

Date :   01 Sep 04 (Deposition) - 31 Aug 06 (Release) - 16 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.23

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

Keywords :   Amine Oxidase, Oxidoreductase, Quinoprotein, Topaquinone Enzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. P. Duff, A. E. Cohen, P. J. Ellis, K. Hilmer, D. B. Langley, D. M. Dooley, H. C. Freeman, J. M. Guss
The 1. 23 A Structure Of Pichia Pastoris Lysyl Oxidase Reveals A Lysine-Lysine Cross-Link
Acta Crystallogr. , Sect. D V. 62 1073 2006
PubMed-ID: 16929109 | Reference-DOI: 10.1107/S0907444906026333

Molecule 1 - LYSYL OXIDASE
	Atcc	:	28485
	Chains	:	A
	EC Number	:	1.4.3.13
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Cell Line	:	GS115
	Expression System Taxid	:	4922
	Expression System Vector	:	PPIC3
	Fragment	:	PPLO HOMOLENZYME HALF DIMER, RESIDUES 41-787
	Organism Scientific	:	PICHIA PASTORIS
	Organism Taxid	:	4922
	Other Details	:	RESIDUE A478 AN ACTIVE SITE TYR RESIDUE, WAS AUTOCATALYTICALLY MODIFIED TO TPQ. THE ENZYME IS GLYCOSYLATED AT ASN A81, ASN A104, ASN A191, ASN A309, AND ASN A 434. RESIDUE LYS 66 IS PARTIALLY CROSS- LINKED WITH RESIDUE LYS 778 TO FORM DEHYDROLYSINONORLEUCINE
	Other Details - Source	:	ISOLATION EXUDATE OF OAK, FRANCE HISTORY, ATCC, CBS, A.GUILLIERMOND

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (8, 22)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	CA	2	Ligand/Ion	CALCIUM ION
3	CL	5	Ligand/Ion	CHLORIDE ION
4	CU	1	Ligand/Ion	COPPER (II) ION
5	IMD	1	Ligand/Ion	IMIDAZOLE
6	MG	5	Ligand/Ion	MAGNESIUM ION
7	NAG	6	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	TPQ	1	Mod. Amino Acid	5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE

Biological Unit 1 (4, 18)

No.	Name	Count	Type	Full Name
1	BMA	2	Ligand/Ion	BETA-D-MANNOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	CU	-1	Ligand/Ion	COPPER (II) ION
5	IMD	2	Ligand/Ion	IMIDAZOLE
6	MG	-1	Ligand/Ion	MAGNESIUM ION
7	NAG	12	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
8	TPQ	2	Mod. Amino Acid	5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE

Asymmetric Unit (19, 19)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:528 , HIS A:530 , HIS A:694 , HOH A:3035	BINDING SITE FOR RESIDUE CU A 801
02	AC2	SOFTWARE	ASP A:537 , LEU A:538 , ASP A:539 , ASP A:683 , ILE A:684 , HOH A:2742	BINDING SITE FOR RESIDUE CA A 802
03	AC3	SOFTWARE	GLU A:580 , PHE A:673 , ASP A:675 , GLU A:677 , HOH A:2903 , HOH A:2904	BINDING SITE FOR RESIDUE CA A 803
04	AC4	SOFTWARE	HOH A:2052 , HOH A:2054 , HOH A:2059 , HOH A:2060 , HOH A:2645 , HOH A:2649	BINDING SITE FOR RESIDUE MG A 804
05	AC5	SOFTWARE	HOH A:2097 , HOH A:2190 , HOH A:2191 , HOH A:2400 , HOH A:2795 , HOH A:2803	BINDING SITE FOR RESIDUE MG A 805
06	AC6	SOFTWARE	HOH A:2024 , HOH A:2252 , HOH A:2551 , HOH A:2552 , HOH A:2556 , HOH A:2561	BINDING SITE FOR RESIDUE MG A 806
07	AC7	SOFTWARE	HOH A:2100 , HOH A:2243 , HOH A:2248 , HOH A:2792 , HOH A:2793	BINDING SITE FOR RESIDUE MG A 807
08	AC8	SOFTWARE	HOH A:2021 , HOH A:2022 , HOH A:2888 , HOH A:2889 , HOH A:2890	BINDING SITE FOR RESIDUE MG A 808
09	AC9	SOFTWARE	LEU A:663 , TYR A:664 , ASP A:665	BINDING SITE FOR RESIDUE CL A 811
10	BC1	SOFTWARE	LYS A:164 , SER A:165 , LYS A:166 , HOH A:2126 , HOH A:2278	BINDING SITE FOR RESIDUE CL A 812
11	BC2	SOFTWARE	ASP A:297 , HOH A:2501 , HOH A:2720 , HOH A:2726	BINDING SITE FOR RESIDUE CL A 813
12	BC3	SOFTWARE	ALA A:573 , ARG A:574 , HOH A:2712 , HOH A:2713	BINDING SITE FOR RESIDUE CL A 814
13	BC4	SOFTWARE	GLY A:420 , TYR A:421 , HOH A:3023	BINDING SITE FOR RESIDUE CL A 815
14	BC5	SOFTWARE	TYR A:396 , ASP A:398 , ILE A:475 , ASN A:477	BINDING SITE FOR RESIDUE IMD A 821
15	BC6	SOFTWARE	ASN A:81 , ASN A:187 , NAG A:1784 , HOH A:3036 , HOH A:3039 , HOH A:3040	BINDING SITE FOR MONO-SACCHARIDE NAG A1780 BOUND TO ASN A 81
16	BC7	SOFTWARE	ASN A:104 , PHE A:158 , THR A:650 , HOH A:2895 , HOH A:3042 , HOH A:3044	BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A1781 THROUGH BMA A1783 BOUND TO ASN A 104
17	BC8	SOFTWARE	ASN A:187 , ASN A:191 , ARG A:196 , NAG A:1780 , HOH A:2317 , HOH A:2337 , HOH A:3040	BINDING SITE FOR MONO-SACCHARIDE NAG A1784 BOUND TO ASN A 191
18	BC9	SOFTWARE	ASP A:302 , ASN A:309 , SER A:311	BINDING SITE FOR MONO-SACCHARIDE NAG A1785 BOUND TO ASN A 309
19	CC1	SOFTWARE	THR A:423 , ASN A:434	BINDING SITE FOR MONO-SACCHARIDE NAG A1786 BOUND TO ASN A 434

Asymmetric Unit

No.	Residues
1	A:45	-	A:756
2	A:212	-	A:233
3	A:415	-	A:440

Asymmetric Unit

No.	Residues
1	Gly A:143	-	Pro A:144
2	Leu A:145	-	Pro A:146
3	Ala A:216	-	Pro A:217
4	Leu A:701	-	Pro A:702

(no "SAP(SNP)/Variant" information available for 1W7C)

(no "PROSITE Motif" information available for 1W7C)

(no "Exon" information available for 1W7C)

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:737
 aligned with Q96X16_PICPA | Q96X16 from UniProtKB/TrEMBL  Length:787

    Alignment length:737
                                    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       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       
         Q96X16_PICPA    43 AECVSNENVEIEAPKTNIWTSLAKEEVQEVLDLLHSTYNITEVTKADFFSNYVLWIETLKPNKTEALTYLDEDGDLPPRNARTVVYFGEGEEGYFEELKVGPLPVSDETTIEPLSFYNTNGKSKLPFEVGHLDRIKSAAKSSFLNKNLNTTIMRDVLEGLIGVPYEDMGCHSAAPQLHDPATGATVDYGTCNINTENDAENLVPTGFFFKFDMTGRDVSQWKMLEYIYNNKVYTSAEELYEAMQKDDFVTLPKIDVDNLDWTVIQRNDSAPIRHLDDRKSPRLVEPEGRRWAYDGEEEYFSWMDWGFYTSWSRDTGISFYDITFKGERIVYELSLQELIAEYGSDDPFNQHTFYSDISYGVGNRFSLVPGYDCPATAGYFTTDTFEYDEFYNRTLSYCVFENQEDYSLLRHTGASYSAITQNPTLNVRFISTIGNYDYNFLYKFFLDGTLEVSVRAAGYIQAGYWNPETSAPYGLKIHDVLSGSFHDHVLNYKVDLDVGGTKNRASKYVMKDVDVEYPWAPGTVYNTKQIAREVLEKEDFNGINWPENGQGILLIESAEETNSFGNPRAYNIMPGGGGVHRIVKNSRSGPETQNWARSNLFLTKHKDEELRSSTALNTNALYDPPVNFNAFLDDESLDGEDIVAWVNLGLHHLPNSNDLPNTIFSTAHASFMLTPFNYFDSENSRDTTQQVFYTYDDETEESNWEFYGNDWSSCGLEVPEPNFEDYTYGRGTRINKK 779
               SCOP domains d1w7ca2 A:43-169 Lysyl oxidase PplO, domains 1 and 2                                                                           d1w7ca3 A:170-315 Lysyl oxidase PplO, domains 1 and 2                                                                                             d1w7ca1 A:316-779 Lysyl oxidase PplO, domain 3                                                                                                                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1w7cA01        1w7cA02 A:58-174  [code=3.10.450.40, no name defined]                                                                1w7cA03 A:175-289  [code=3.10.450.40, no name defined]                                                             1w7cA01 A:43-57,A:290-779 Copper amine oxidase, Domain 3                                                                                                                                                                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------Cu_amine_oxidN2-1w7cA01 A:62-151                                                          ---------------------------------------------------------------------------------------DUF1965-1w7cA03 A:239-314                                                   --------Cu_amine_oxid-1w7cA02 A:323-734                                                                                                                                                                                                                                                                                                                                                                                             --------------------------------------------- Pfam domains
         Sec.struct. author ........ee............hhhhhhhhhhhhhhhh...hhhhh....eeeeeeeee..hhhhhhhhhhh.......eeeeeeee......eeeeeeee........eeee..........eee.hhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.eeeee....ee......eeeeeeeee.....hhhh.eeeeeeeee....hhhhheeeeeee..eee.hhhhhhhhhhh.............hhhhh............................eee....eeee..eeeeeeee...eeeeeeeee..eeeeeeeeeeeeeeee.....hhhh.eeehhhhh................................................eeeee..eeeee..........................................ee.....hhhhh.eee..ee...eeeeeeeeeee.................................................hhhh...........................................hhhhhh............................hhhhhh.......eeeeeeeeeeeee..hhhhh..............................eeeeee......eeee................hhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w7c A  43 AECVSNENVEIEAPKTNIWTSLAKEEVQEVLDLLHSTYNITEVTKADFFSNYVLWIETLKPNKTEALTYLDEDGDLPPRNARTVVYFGEGEEGYFEELKVGPLPVSDETTIEPLSFYNTNGKSKLPFEVGHLDRIKSAAKSSFLNKNLNTTIMRDVLEGLIGVPYEDMGCHSAAPQLHDPATGATVDYGTCNINTENDAENLVPTGFFFKFDMTGRDVSQWKMLEYIYNNKVYTSAEELYEAMQKDDFVTLPKIDVDNLDWTVIQRNDSAPVRHLDDRKSPRLVEPEGRRWAYDGDEEYFSWMDWGFYTSWSRDTGISFYDITFKGERIVYELSLQELIAEYGSDDPFNQHTFYSDISYGVGNRFSLVPGYDCPSTAGYFTTDTFEYDEFYNRTLSYCVFENQEDYSLLRHTGASYSAITQNPTLNVRFISTIGNyDYNFLYKFFLDGTLEVSVRAAGYIQAGYWNPETSAPYGLKIHDVLSGSFHDHVLNYKVDLDVGGTKNRASQYVMKDVDVEYPWAPGTVYNTKQIAREVFENEDFNGINWPENGQGILLIESAEETNSFGNPRAYNIMPGGGGVHRIVKNSRSGPETQNWARSNLFLTKHKDTELRSSTALNTNALYDPPVNFNAFLDDESLDGEDIVAWVNLGLHHLPNSNDLPNTIFSTAHASFMLTPFNYFDSENSRDTTQQVFYTYDDETEESNWEFYGNDWSSCGVEVAEPNFEDYTYGRGTRINKK 779
                                    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       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             478-TPQ

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Nuclear Transport Factor 2; Chain: A, (517)

Homologous Superfamily: [code=3.10.450.40, no name defined] (77)

Pichia pastoris. Organism_taxid: 4922. (2)

1a	1w7cA03	A:175-289
1b	1w7cA02	A:58-174

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Beta-galactosidase; Chain A, domain 5 (250)

Homologous Superfamily: Copper amine oxidase, Domain 3 (74)

Pichia pastoris. Organism_taxid: 4922. (2)

1w7cA01

A:43-57,A:290-779

Asymmetric Unit(hide GO term definitions)

Chain A (Q96X16_PICPA | Q96X16)

molecular function
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	GO:0052597	diamine oxidase activity	Catalysis of the reaction: a diamine + H2O + O2 = a monoamine + NH3 + hydrogen peroxide.
	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.
	GO:0008131	primary amine oxidase activity	Catalysis of the reaction: a primary amine + H2O + O2 = an aldehyde + NH3 + hydrogen peroxide.
	GO:0048038	quinone binding	Interacting selectively and non-covalently with a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
biological process
	GO:0009308	amine metabolic process	The chemical reactions and pathways involving any organic compound that is weakly basic in character and contains an amino or a substituted amino group. Amines are called primary, secondary, or tertiary according to whether one, two, or three carbon atoms are attached to the nitrogen atom.
	GO:0071241	cellular response to inorganic substance	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an inorganic substance stimulus.
	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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	Cis Peptide Bonds
		Ala A:216 - Pro A:217	[ RasMol ]
		Gly A:143 - Pro A:144	[ RasMol ]
		Leu A:145 - Pro A:146	[ RasMol ]
		Leu A:701 - Pro A:702	[ RasMol ]

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	Q96X16_PICPA \| Q96X16	:	1n9e 1rky

1n9e	CRYSTAL STRUCTURE OF PICHIA PASTORIS LYSYL OXIDASE PPLO

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (8, 22)

Sites (19, 19)

SS Bonds (3, 3)

Cis Peptide Bonds (4, 4)

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