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(-) Description

Title :  PPLO + XE
 
Authors :  J. M. Guss, A. P. Duff
Date :  24 Nov 03  (Deposition) - 07 Dec 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Pplo, Lysyl Oxidase, Cao, Cuao, Copper-Containing, Amine Oxidase, Oxygen Binding Site, Dioxygen Binding Site, Xenon, Tpq, Quinone, Trihydroxyphenylalanine Quinone, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Duff, D. M. Trambaiolo, A. E. Cohen, P. J. Ellis, G. A. Juda, E. M. Shepard, D. B. Langley, D. M. Dooley, H. C. Freeman, J. M. Guss
Using Xenon As A Probe For Dioxygen-Binding Sites In Copper Amine Oxidases
J. Mol. Biol. V. 344 599 2004
PubMed-ID: 15533431  |  Reference-DOI: 10.1016/J.JMB.2004.09.075

(-) Compounds

Molecule 1 - LYSYL OXIDASE
    Chains: A
    EC Number: 1.4.3.13
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC3
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 41-787
    Gene: ATCC 28, 485
    Organism Scientific: PICHIA PASTORIS
    Organism Taxid: 4922
    Synonym: PPLO

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 29)

Asymmetric Unit (9, 29)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2CA2Ligand/IonCALCIUM ION
3CL6Ligand/IonCHLORIDE ION
4CU1Ligand/IonCOPPER (II) ION
5IMD1Ligand/IonIMIDAZOLE
6MG3Ligand/IonMAGNESIUM ION
7NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
8TPQ1Mod. Amino Acid5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
9XE8Ligand/IonXENON
Biological Unit 1 (4, 18)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4CU-1Ligand/IonCOPPER (II) ION
5IMD2Ligand/IonIMIDAZOLE
6MG-1Ligand/IonMAGNESIUM ION
7NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
8TPQ2Mod. Amino Acid5-(2-CARBOXY-2-AMINOETHYL)-2-HYDROXY-1,4-BENZOQUINONE
9XE-1Ligand/IonXENON

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:79 , ASN A:81 , ASN A:187 , LYS A:188 , ASN A:191 , NAG A:1191 , HOH A:2492 , HOH A:2567BINDING SITE FOR RESIDUE NAG A 1081
02AC2SOFTWAREASN A:104 , GLU A:107 , PHE A:158 , THR A:650 , NAG A:1105 , HOH A:2355 , HOH A:2404 , HOH A:2622BINDING SITE FOR RESIDUE NAG A 1104
03AC3SOFTWAREPHE A:158 , NAG A:1104 , BMA A:1106 , HOH A:2510BINDING SITE FOR RESIDUE NAG A 1105
04AC4SOFTWARENAG A:1105BINDING SITE FOR RESIDUE BMA A 1106
05AC5SOFTWAREASN A:187 , ASN A:191 , ARG A:196 , NAG A:1081 , HOH A:2567BINDING SITE FOR RESIDUE NAG A 1191
06AC6SOFTWAREASP A:302 , ASN A:309 , SER A:311BINDING SITE FOR RESIDUE NAG A 1309
07AC7SOFTWAREASN A:434BINDING SITE FOR RESIDUE NAG A 1434
08AC8SOFTWARETPQ A:478 , HIS A:528 , HIS A:530 , HIS A:694BINDING SITE FOR RESIDUE CU A 801
09AC9SOFTWAREASP A:537 , LEU A:538 , ASP A:539 , ASP A:683 , ILE A:684 , HOH A:2455BINDING SITE FOR RESIDUE CA A 802
10BC1SOFTWAREGLU A:580 , PHE A:673 , ASP A:675 , GLU A:677 , HOH A:2356 , HOH A:2615BINDING SITE FOR RESIDUE CA A 803
11BC2SOFTWAREHOH A:2306 , HOH A:2534 , HOH A:2589 , HOH A:2609 , HOH A:2611 , HOH A:2614BINDING SITE FOR RESIDUE MG A 804
12BC3SOFTWAREHOH A:2362BINDING SITE FOR RESIDUE MG A 805
13BC4SOFTWAREHOH A:2313 , HOH A:2380 , HOH A:2440 , HOH A:2617BINDING SITE FOR RESIDUE MG A 806
14BC5SOFTWARETYR A:664 , ASP A:665 , HOH A:2200 , HOH A:2461BINDING SITE FOR RESIDUE CL A 811
15BC6SOFTWARELYS A:164 , SER A:165 , LYS A:166 , HOH A:2470BINDING SITE FOR RESIDUE CL A 812
16BC7SOFTWAREASP A:297 , HOH A:2107 , HOH A:2233 , HOH A:2485BINDING SITE FOR RESIDUE CL A 813
17BC8SOFTWAREALA A:573 , ARG A:574BINDING SITE FOR RESIDUE CL A 814
18BC9SOFTWARETYR A:421 , HOH A:2606BINDING SITE FOR RESIDUE CL A 815
19CC1SOFTWAREPHE A:91 , ASP A:259BINDING SITE FOR RESIDUE CL A 816
20CC2SOFTWARETYR A:396 , ASP A:398 , ASN A:477 , HOH A:2632BINDING SITE FOR RESIDUE IMD A 821
21CC3SOFTWAREILE A:371BINDING SITE FOR RESIDUE XE A 901
22CC4SOFTWAREMET A:265 , LEU A:266 , TYR A:268 , THR A:276BINDING SITE FOR RESIDUE XE A 902
23CC5SOFTWAREXE A:907 , XE A:908BINDING SITE FOR RESIDUE XE A 903
24CC6SOFTWARETYR A:413 , ASP A:447 , HOH A:2634BINDING SITE FOR RESIDUE XE A 904
25CC7SOFTWARELYS A:66BINDING SITE FOR RESIDUE XE A 906
26CC8SOFTWARELEU A:532 , GLY A:691 , XE A:903 , XE A:908BINDING SITE FOR RESIDUE XE A 907
27CC9SOFTWAREXE A:903 , XE A:907BINDING SITE FOR RESIDUE XE A 908

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (4, 4)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1RKY)

(-) Sequences/Alignments

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:735
 aligned with Q96X16_PICPA | Q96X16 from UniProtKB/TrEMBL  Length:787

    Alignment length:735
                                    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 AECVSNENVEIEAPKTNIWTSLAKEEVQEVLDLLHSTYNITEVTKADFFSNYVLWIETLKPNKTEALTYLDEDGDLPPRNARTVVYFGEGEEGYFEELKVGPLPVSDETTIEPLSFYNTNGKSKLPFEVGHLDRIKSAAKSSFLNKNLNTTIMRDVLEGLIGVPYEDMGCHSAAPQLHDPATGATVDYGTCNINTENDAENLVPTGFFFKFDMTGRDVSQWKMLEYIYNNKVYTSAEELYEAMQKDDFVTLPKIDVDNLDWTVIQRNDSAPIRHLDDRKSPRLVEPEGRRWAYDGEEEYFSWMDWGFYTSWSRDTGISFYDITFKGERIVYELSLQELIAEYGSDDPFNQHTFYSDISYGVGNRFSLVPGYDCPATAGYFTTDTFEYDEFYNRTLSYCVFENQEDYSLLRHTGASYSAITQNPTLNVRFISTIGNYDYNFLYKFFLDGTLEVSVRAAGYIQAGYWNPETSAPYGLKIHDVLSGSFHDHVLNYKVDLDVGGTKNRASKYVMKDVDVEYPWAPGTVYNTKQIAREVLEKEDFNGINWPENGQGILLIESAEETNSFGNPRAYNIMPGGGGVHRIVKNSRSGPETQNWARSNLFLTKHKDEELRSSTALNTNALYDPPVNFNAFLDDESLDGEDIVAWVNLGLHHLPNSNDLPNTIFSTAHASFMLTPFNYFDSENSRDTTQQVFYTYDDETEESNWEFYGNDWSSCGLEVPEPNFEDYTYGRGTRIN 777
               SCOP domains d1rkya2 A:43-169 Lysyl oxidase PplO, domains 1 and 2                                                                           d1rkya3 A:170-315 Lysyl oxidase PplO, domains 1 and 2                                                                                             d1rkya1 A:316-777 Lysyl oxidase PplO, domain 3                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 1rkyA01        1rkyA02 A:58-174  [code=3.10.450.40, no name defined]                                                                1rkyA03 A:175-289  [code=3.10.450.40, no name defined]                                                             1rkyA01 A:43-57,A:290-777 Copper amine oxidase, Domain 3                                                                                                                                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains -------------------Cu_amine_oxidN2-1rkyA01 A:62-151                                                          ---------------------------------------------------------------------------------------DUF1965-1rkyA03 A:239-314                                                   --------Cu_amine_oxid-1rkyA02 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..eeeeeeeeeeeeeeeee....hhhh.eeehhhhh.................eeeeeeeee..eeeeeeeeeeeeeee.....eeeee..eeeee..eeeeeeeee......eeeeeee.....eeeeeee......ee.....hhh.eeeee..eeeeeeeeeeeeeeee.....eeeeeeeeeeeeeee.......eeeeeeeeeeee..........hhhh.eeeeeeeeeee.....eeeeeeee..................hhhhhh.eeeee......................hhhhhh.......eeeeeeeeeeeee..hhhhh........eeeeeeeee.............eeeeee......eeee................hhhhh.....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rky A  43 AECVSNENVEIEAPKTNIWTSLAKEEVQEVLDLLHSTYNITEVTKADFFSNYVLWIETLKPNKTEALTYLDEDGDLPPRNARTVVYFGEGEEGYFEELKVGPLPVSDETTIEPLSFYNTNGKSKLPFEVGHLDRIKSAAKSSFLNKNLNTTIMRDVLEGLIGVPYEDMGCHSAAPQLHDPATGATVDYGTCNINTENDAENLVPTGFFFKFDMTGRDVSQWKMLEYIYNNKVYTSAEELYEAMQKDDFVTLPKIDVDNLDWTVIQRNDSAPVRHLDDRKSPRLVEPEGRRWAYDGDEEYFSWMDWGFYTSWSRDTGISFYDITFKGERIVYELSLQELIAEYGSDDPFNQHTFYSDISYGVGNRFSLVPGYDCPSTAGYFTTDTFEYDEFYNRTLSYCVFENQEDYSLLRHTGASYSAITQNPTLNVRFISTIGNyDYNFLYKFFLDGTLEVSVRAAGYIQAGYWNPETSAPYGLKIHDVLSGSFHDHVLNYKVDLDVGGTKNRASQYVMKDVDVEYPWAPGTVYNTKQIAREVFENEDFNGINWPENGQGILLIESAEETNSFGNPRAYNIMPGGGGVHRIVKNSRSGPETQNWARSNLFLTKHKDTELRSSTALNTNALYDPPVNFNAFLDDESLDGEDIVAWVNLGLHHLPNSNDLPNTIFSTAHASFMLTPFNYFDSENSRDTTQQVFYTYDDETEESNWEFYGNDWSSCGVEVAEPNFEDYTYGRGTRIN 777
                                    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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 3)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: CuAO_N2_N3 (40)
(-)
Clan: no clan defined [family: Cu_amine_oxid] (40)
(-)
Clan: no clan defined [family: DUF1965] (3)

(-) Gene Ontology  (9, 9)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q96X16_PICPA | Q96X16: 1n9e 1w7c

(-) Related Entries Specified in the PDB File

1n9e PPLO NATIVE HOLOENZYME
1rjo AGAO + XE