1ASP - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURES AND MECHANISTIC IMPLICATIONS OF THREE FUNCTIONAL DERIVATIVES OF ASCORBATE OXIDASE FROM ZUCCHINI: REDUCED-, PEROXIDE-, AND AZIDE-FORMS

Authors :   A. Messerschmidt, H. Luecke, R. Huber

Date :   25 Nov 92 (Deposition) - 31 Jan 94 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.59

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

Keywords :   Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Messerschmidt, H. Luecke, R. Huber
X-Ray Structures And Mechanistic Implications Of Three Functional Derivatives Of Ascorbate Oxidase From Zucchini. Reduced, Peroxide And Azide Forms.
J. Mol. Biol. V. 230 997 1993
PubMed-ID: 8478945 | Reference-DOI: 10.1006/JMBI.1993.1215
(for further references see the PDB file header)

Molecule 1 - ASCORBATE OXIDASE
	Chains	:	A, B
	EC Number	:	1.10.3.3
	Engineered	:	YES
	Organism Common	:	ZUCCHINI
	Organism Scientific	:	CUCURBITA PEPO VAR. MELOPEPO
	Organism Taxid	:	3665
	Strain	:	VAR. MELOPEPO

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 15)

No.	Name	Count	Type	Full Name
1	CU	9	Ligand/Ion	COPPER (II) ION
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	OH	2	Ligand/Ion	HYDROXIDE ION
4	PEO	2	Ligand/Ion	HYDROGEN PEROXIDE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	OH	-1	Ligand/Ion	HYDROXIDE ION
4	PEO	2	Ligand/Ion	HYDROGEN PEROXIDE

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	CU	-1	Ligand/Ion	COPPER (II) ION
2	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	OH	-1	Ligand/Ion	HYDROXIDE ION
4	PEO	4	Ligand/Ion	HYDROGEN PEROXIDE

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:71 , ASN A:92 , PRO A:532 , HOH A:953	BINDING SITE FOR RESIDUE NAG A 553
02	AC2	SOFTWARE	VAL B:45 , ASN B:92 , PRO B:532	BINDING SITE FOR RESIDUE NAG B 553
03	AC3	SOFTWARE	HIS A:445 , CYS A:507 , HIS A:512 , MET A:517	BINDING SITE FOR RESIDUE CU A 554
04	AC4	SOFTWARE	HIS A:106 , HIS A:450 , HIS A:506 , PEO A:560	BINDING SITE FOR RESIDUE CU A 555
05	AC5	SOFTWARE	HIS A:62 , HIS A:104 , HIS A:508 , PEO A:560	BINDING SITE FOR RESIDUE CU A 556
06	AC6	SOFTWARE	HIS A:60 , HIS A:448 , HIS A:450 , OH A:558	BINDING SITE FOR RESIDUE CU A 557
07	AC7	SOFTWARE	HIS A:60 , GLY A:63 , HIS A:448 , CU A:557 , HOH A:642 , HOH A:772	BINDING SITE FOR RESIDUE OH A 558
08	AC8	SOFTWARE	HIS B:445 , CYS B:507 , HIS B:512 , MET B:517	BINDING SITE FOR RESIDUE CU B 554
09	AC9	SOFTWARE	HIS B:106 , HIS B:450 , HIS B:506 , PEO B:559	BINDING SITE FOR RESIDUE CU B 555
10	BC1	SOFTWARE	HIS B:62 , HIS B:104 , HIS B:508 , PEO B:559	BINDING SITE FOR RESIDUE CU B 556
11	BC2	SOFTWARE	HIS B:60 , HIS B:62 , HIS B:448 , HIS B:450 , OH B:558	BINDING SITE FOR RESIDUE CU B 557
12	BC3	SOFTWARE	HIS B:60 , HIS B:62 , GLY B:63 , HIS B:448 , CU B:557 , HOH B:659	BINDING SITE FOR RESIDUE OH B 558
13	BC4	SOFTWARE	HIS A:286 , HIS B:286	BINDING SITE FOR RESIDUE CU A 559
14	BC5	SOFTWARE	HIS A:104 , HIS A:106 , HIS A:450 , HIS A:506 , HIS A:508 , CU A:555 , CU A:556	BINDING SITE FOR RESIDUE PEO A 560
15	BC6	SOFTWARE	HIS B:104 , HIS B:106 , HIS B:506 , HIS B:508 , CU B:555 , CU B:556	BINDING SITE FOR RESIDUE PEO B 559

Asymmetric Unit

No.	Residues
1	A:19	-	A:201
2	A:81	-	A:538
3	A:180	-	A:193
4	B:19	-	B:201
5	B:81	-	B:538
6	B:180	-	B:193

Asymmetric Unit

No.	Residues
1	Phe A:31	-	Pro A:32
2	Lys A:159	-	Pro A:160
3	Leu A:299	-	Pro A:300
4	Phe B:31	-	Pro B:32
5	Lys B:159	-	Pro B:160
6	Leu B:299	-	Pro B:300

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTICOPPER_OXIDASE1	PS00079	Multicopper oxidases signature 1.	ASO_CUCPM	501-521	2	A:501-521 B:501-521
2	MULTICOPPER_OXIDASE2	PS00080	Multicopper oxidases signature 2.	ASO_CUCPM	506-517	2	A:506-517 B:506-517

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTICOPPER_OXIDASE1	PS00079	Multicopper oxidases signature 1.	ASO_CUCPM	501-521	2	A:501-521 B:501-521
2	MULTICOPPER_OXIDASE2	PS00080	Multicopper oxidases signature 2.	ASO_CUCPM	506-517	2	A:506-517 B:506-517

Biological Unit 2 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MULTICOPPER_OXIDASE1	PS00079	Multicopper oxidases signature 1.	ASO_CUCPM	501-521	4	A:501-521 B:501-521
2	MULTICOPPER_OXIDASE2	PS00080	Multicopper oxidases signature 2.	ASO_CUCPM	506-517	4	A:506-517 B:506-517

(no "Exon" information available for 1ASP)

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:552
 aligned with ASO_CUCPM | P37064 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:552
                                    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       500       510       520       530       540       550  
            ASO_CUCPM     1 SQIRHYKWEVEYMFWAPNCNENIVMGINGQFPGPTIRANAGDSVVVELTNKLHTEGVVIHWHGILQRGTPWADGTASISQCAINPGETFFYNFTVDNPGTFFYHGHLGMQRSAGLYGSLIVDPPQGKKEPFHYDGEINLLLSDWWHQSIHKQEVGLSSKPIRWIGEPQTILLNGRGQFDCSIAAKYDSNLEPCKLKGSESCAPYIFHVSPKKTYRIRIASTTALAALNFAIGNHQLLVVEADGNYVQPFYTSDIDIYSGESYSVLITTDQNPSENYWVSVGTRARHPNTPPGLTLLNYLPNSVSKLPTSPPPQTPAWDDFDRSKNFTYRITAAMGSPKPPVKFNRRIFLLNTQNVINGYVKWAINDVSLALPPTPYLGAMKYNLLHAFDQNPPPEVFPEDYDIDTPPTNEKTRIGNGVYQFKIGEVVDVILQNANMMKENLSETHPWHLHGHDFWVLGYGDGKFSAEEESSLNLKNPPLRNTVVIFPYGWTAIRFVADNPGVWAFHCHIEPHLHMGMGVVFAEGVEKVGRIPTKALACGGTAKSLINNPKNP 552
               SCOP domains d1aspa1 A:1-129 Ascorbate oxidase                                                                                                d1aspa2 A:130-338 Ascorbate oxidase                                                                                                                                                                              d1aspa3 A:339-552 Ascorbate oxidase                                                                                                                                                                                    SCOP domains
               CATH domains 1aspA01 A:1-130 Cupredoxins -  blue copper proteins                                                                               1aspA02 A:131-336 Cupredoxins -  blue copper proteins                                                                                                                                                         1aspA03 A:337-552 Cupredoxins -  blue copper proteins                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......eeeeee........eeee...eeeeeeee........eeee......hhhhh..............eeeeeee....eeeeeee....hhhhh.eeeeeee............eeeeeeeeee...hhhhhhhhh............eeee..........hhhhh..................eee....eeeeeeee.....eeeeee....eeeeee..eeeeeeee..eee....eeeeeee........eeeeeeee........eeeeeee....................hhhhhhhhhhh...............eeeeeeeeeeee..eeeeee..eee.....hhhhhhhh..............................eee...eee....eeeeeee............eeeee....eeeeeeee...hhhhhhhh......ee.eeee...eeeeeeee....eeeeeee.hhhhhhh..eeeeee.hhhh...hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 ------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_----------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1asp A   1 SQIRHYKWEVEYMFWAPNCNENIVMGINGQFPGPTIRANAGDSVVVELTNKLHTEGVVIHWHGILQRGTPWADGTASISQCAINPGETFFYNFTVDNPGTFFYHGHLGMQRSAGLYGSLIVDPPQGKKEPFHYDGEINLLLSDWWHQSIHKQEVGLSSKPIRWIGEPQTILLNGRGQFDCSIAAKYDSNLEPCKLKGSESCAPYIFHVSPKKTYRIRIASTTALAALNFAIGNHQLLVVEADGNYVQPFYTSDIDIYSGESYSVLITTDQNPSENYWVSVGTRARHPNTPPGLTLLNYLPNSVSKLPTSPPPQTPAWDDFDRSKNFTYRITAAMGSPKPPVKFNRRIFLLNTQNVINGYVKWAINDVSLALPPTPYLGAMKYNLLHAFDQNPPPEVFPEDYDIDTPPTNEKTRIGNGVYQFKIGEVVDVILQNANMMKENLSETHPWHLHGHDFWVLGYGDGKFSAEEESSLNLKNPPLRNTVVIFPYGWTAIRFVADNPGVWAFHCHIEPHLHMGMGVVFAEGVEKVGRIPTKALACGGTAKSLINNPKNP 552
                                    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       500       510       520       530       540       550

Chain B from PDB  Type:PROTEIN  Length:552
 aligned with ASO_CUCPM | P37064 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:552
                                    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       500       510       520       530       540       550  
            ASO_CUCPM     1 SQIRHYKWEVEYMFWAPNCNENIVMGINGQFPGPTIRANAGDSVVVELTNKLHTEGVVIHWHGILQRGTPWADGTASISQCAINPGETFFYNFTVDNPGTFFYHGHLGMQRSAGLYGSLIVDPPQGKKEPFHYDGEINLLLSDWWHQSIHKQEVGLSSKPIRWIGEPQTILLNGRGQFDCSIAAKYDSNLEPCKLKGSESCAPYIFHVSPKKTYRIRIASTTALAALNFAIGNHQLLVVEADGNYVQPFYTSDIDIYSGESYSVLITTDQNPSENYWVSVGTRARHPNTPPGLTLLNYLPNSVSKLPTSPPPQTPAWDDFDRSKNFTYRITAAMGSPKPPVKFNRRIFLLNTQNVINGYVKWAINDVSLALPPTPYLGAMKYNLLHAFDQNPPPEVFPEDYDIDTPPTNEKTRIGNGVYQFKIGEVVDVILQNANMMKENLSETHPWHLHGHDFWVLGYGDGKFSAEEESSLNLKNPPLRNTVVIFPYGWTAIRFVADNPGVWAFHCHIEPHLHMGMGVVFAEGVEKVGRIPTKALACGGTAKSLINNPKNP 552
               SCOP domains d1aspb1 B:1-129 Ascorbate oxidase                                                                                                d1aspb2 B:130-338 Ascorbate oxidase                                                                                                                                                                              d1aspb3 B:339-552 Ascorbate oxidase                                                                                                                                                                                    SCOP domains
               CATH domains 1aspB01 B:1-130 Cupredoxins -  blue copper proteins                                                                               1aspB02 B:131-336 Cupredoxins -  blue copper proteins                                                                                                                                                         1aspB03 B:337-552 Cupredoxins -  blue copper proteins                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeee......eeeeee........eeee...eeeeeeee........eeee......hhhhh..............eeeeeee....eeeeeee..........eeeeeee............eeeeeeeeee...hhhhhhhhhhh..........eeee..........hhhhh..................eee....eeeeeeee.....eeeeee....eeeeee..eeeeeeee..eee....eeeeeee........eeeeeeee........eeeeeee....................hhhhhhhhhh................eeeeeeeeeeee..eeeeee..eee.....hhhhhhhh..............................eee...eee....eeeeeee............eeeee....eeeeeeee...hhhhhhhh......ee.eeee...eeeeeeee....eeeeeee.hhhhhhh..eeeeee.hhhh...hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_OXIDASE1 ------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MULTICOPPER_----------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1asp B   1 SQIRHYKWEVEYMFWAPNCNENIVMGINGQFPGPTIRANAGDSVVVELTNKLHTEGVVIHWHGILQRGTPWADGTASISQCAINPGETFFYNFTVDNPGTFFYHGHLGMQRSAGLYGSLIVDPPQGKKEPFHYDGEINLLLSDWWHQSIHKQEVGLSSKPIRWIGEPQTILLNGRGQFDCSIAAKYDSNLEPCKLKGSESCAPYIFHVSPKKTYRIRIASTTALAALNFAIGNHQLLVVEADGNYVQPFYTSDIDIYSGESYSVLITTDQNPSENYWVSVGTRARHPNTPPGLTLLNYLPNSVSKLPTSPPPQTPAWDDFDRSKNFTYRITAAMGSPKPPVKFNRRIFLLNTQNVINGYVKWAINDVSLALPPTPYLGAMKYNLLHAFDQNPPPEVFPEDYDIDTPPTNEKTRIGNGVYQFKIGEVVDVILQNANMMKENLSETHPWHLHGHDFWVLGYGDGKFSAEEESSLNLKNPPLRNTVVIFPYGWTAIRFVADNPGVWAFHCHIEPHLHMGMGVVFAEGVEKVGRIPTKALACGGTAKSLINNPKNP 552
                                    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       500       510       520       530       540       550

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Cupredoxin-like (545)

Superfamily: Cupredoxins (543)

Family: Multidomain cupredoxins (146)

Protein domain: Ascorbate oxidase (4)

Zucchini (Cucurbita pepo var. medullosa) [TaxId: 3663] (4)

1a	d1aspa1	A:1-129
1b	d1aspa2	A:130-338
1c	d1aspa3	A:339-552
1d	d1aspb1	B:1-129
1e	d1aspb2	B:130-338
1f	d1aspb3	B:339-552

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Cupredoxins - blue copper proteins (420)

Melopepo (Cucurbita pepo var) (4)

1a	1aspA01	A:1-130
1b	1aspA02	A:131-336
1c	1aspB02	B:131-336
1d	1aspA03	A:337-552
1e	1aspB03	B:337-552
1f	1aspB01	B:1-130

(no "Pfam Domain" information available for 1ASP)

Asymmetric Unit(hide GO term definitions)

Chain A,B (ASO_CUCPM | P37064)

molecular function
	GO:0008447	L-ascorbate oxidase activity	Catalysis of the reaction: 2 L-ascorbate + O2 = 2 dehydroascorbate + 2 H2O.
	GO:0005507	copper ion binding	Interacting selectively and non-covalently with copper (Cu) ions.
	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.
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 Unit
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	1asp
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	ASO_CUCPM \| P37064	:	1aoz 1aso 1asq

(no "Related Entries Specified in the PDB File" available for 1ASP)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 15)

Sites (15, 15)

SS Bonds (6, 6)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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