1BT1 - JenaLib

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Title :   CATECHOL OXIDASE FROM IPOMOEA BATATAS (SWEET POTATOES) IN THE NATIVE CU(II)-CU(II) STATE

Authors :   T. Klabunde, C. Eicken, J. C. Sacchettini, B. Krebs

Date :   02 Sep 98 (Deposition) - 02 Sep 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Catechol Oxidase, Dicopper Enzyme, Ipomoea Batatas, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Klabunde, C. Eicken, J. C. Sacchettini, B. Krebs
Crystal Structure Of A Plant Catechol Oxidase Containing A Dicopper Center.
Nat. Struct. Biol. V. 5 1084 1998
PubMed-ID: 9846879 | Reference-DOI: 10.1038/4193
(for further references see the PDB file header)

Molecule 1 - PROTEIN (CATECHOL OXIDASE)
	Chains	:	A, B
	EC Number	:	1.10.3.1
	Organ	:	MATURE TUBER
	Organism Common	:	SWEET POTATO
	Organism Scientific	:	IPOMOEA BATATAS
	Organism Taxid	:	4120
	Other Details	:	COVALENT THIOETHER BOND BETWEEN H109 AND C92
	Synonym	:	O-DIPHENOL OXIDASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	C2O	2	Ligand/Ion	CU-O-CU LINKAGE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	C2O	1	Ligand/Ion	CU-O-CU LINKAGE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	C2O	1	Ligand/Ion	CU-O-CU LINKAGE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:88 , HIS A:109 , HIS A:118 , HIS A:240 , HIS A:244 , PHE A:261 , HIS A:274	BINDING SITE FOR RESIDUE C2O A 500
2	AC2	SOFTWARE	HIS B:88 , HIS B:109 , HIS B:118 , HIS B:240 , HIS B:244 , PHE B:261 , HIS B:274	BINDING SITE FOR RESIDUE C2O B 500
3	CU1	AUTHOR	HIS A:88 , HIS A:109 , HIS A:118	BINDING SITE FOR COPPER A IN MONOMER A
4	CU2	AUTHOR	HIS B:88 , HIS B:109 , HIS B:118	BINDING SITE FOR COPPER A IN MONOMER B
5	CU3	AUTHOR	HIS A:240 , HIS A:244 , HIS A:274	BINDING SITE FOR COPPER B IN MONOMER A
6	CU4	AUTHOR	HIS B:240 , HIS B:244 , HIS B:274	BINDING SITE FOR COPPER B IN MONOMER B

Asymmetric Unit

No.	Residues
1	A:11	-	A:28
2	A:27	-	A:89
3	B:11	-	B:28
4	B:27	-	B:89

Asymmetric Unit

No.	Residues
1	Val A:13	-	Pro A:14
2	Val B:13	-	Pro B:14

(no "SAP(SNP)/Variant" information available for 1BT1)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYROSINASE_1	PS00497	Tyrosinase CuA-binding region signature.	PPO1_IPOBA	109-126	2	A:109-126 B:109-126

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYROSINASE_1	PS00497	Tyrosinase CuA-binding region signature.	PPO1_IPOBA	109-126	1	A:109-126 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TYROSINASE_1	PS00497	Tyrosinase CuA-binding region signature.	PPO1_IPOBA	109-126	1	- B:109-126

(no "Exon" information available for 1BT1)

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:336
 aligned with PPO1_IPOBA | Q9ZP19 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:341
                                    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 
           PPO1_IPOBA     1 APIQAPEISKCVVPPADLPPGAVVDNCCPPVASNIVDYKLPAVTTMKVRPAAHTMDKDAIAKFAKAVELMKALPADDPRNFYQQALVHCAYCNGGYDQVNFPDQEIQVHNSWLFFPFHRWYLYFYERILGKLIGDPSFGLPFWNWDNPGGMVLPDFLNDSTSSLYDSNRNQSHLPPVVVDLGYNGADTDVTDQQRITDNLALMYKQMVTNAGTAELFLGKAYRAGDAPSPGAGSIETSPHIPIHRWVGDPRNTNNEDMGNFYSAGRDIAFYCHHSNVDRMWTIWQQLAGKPRKRDYTDSDWLNATFLFYDENGQAVKVRIGDSLDNQKMGYKYAKTPLPWL 341
               SCOP domains d1bt1a_ A: Catechol oxidase                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1bt1A00 A:1-341 Di-copper center containing domain from catechol oxidase                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh........................eee.........eee..hhh..hhhhhhhhhhhhhhh.........hhhhhhhhhhhh.....................hhhhhhhhhhhhhhhhhhh...............hhh....hhhh.................................hhhhhhhhhhhhhhhh.hhh..hhhhh...............hhhh..hhhhhhhh................hhh.hhhhhhhhhhhhhhhhhhh..-----.....hhhh..eeeee.....eeeeehhhh...hhh.eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------TYROSINASE_1      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bt1 A   1 APIQAPEISKCVVPPADLPPGAVVDNCCPPVASNIVDYKLPAVTTMKVRPAAHTMDKDAIAKFAKAVELMKALPADDPRNFYQQALVHCAYCNGGYDQVNFPDQEIQVHNSWLFFPFHRWYLYFYERILGKLIGDPSFGLPFWNWDNPGGMVLPDFLNDSTSSLYDSNRNQSHLPPVVVDLGYNGADTDVTDQQRITDNLALMYKQMVTNAGTAELFLGKAYRAGDAPSPGAGSIETSPHIPIHRWVGDPRNTNNEDMGNFYSAGRDIAFYCHHSNVDRMWTIWQQLA-----RDYTDSDWLNATFLFYDENGQAVKVRIGDSLDNQKMGYKYAKTPLPWL 341
                                    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       | -   |   300       310       320       330       340 
                                                                                                                                                                                                                                                                                                                         288   294

Chain B from PDB  Type:PROTEIN  Length:336
 aligned with PPO1_IPOBA | Q9ZP19 from UniProtKB/Swiss-Prot  Length:496

    Alignment length:341
                                    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 
           PPO1_IPOBA     1 APIQAPEISKCVVPPADLPPGAVVDNCCPPVASNIVDYKLPAVTTMKVRPAAHTMDKDAIAKFAKAVELMKALPADDPRNFYQQALVHCAYCNGGYDQVNFPDQEIQVHNSWLFFPFHRWYLYFYERILGKLIGDPSFGLPFWNWDNPGGMVLPDFLNDSTSSLYDSNRNQSHLPPVVVDLGYNGADTDVTDQQRITDNLALMYKQMVTNAGTAELFLGKAYRAGDAPSPGAGSIETSPHIPIHRWVGDPRNTNNEDMGNFYSAGRDIAFYCHHSNVDRMWTIWQQLAGKPRKRDYTDSDWLNATFLFYDENGQAVKVRIGDSLDNQKMGYKYAKTPLPWL 341
               SCOP domains d1bt1b_ B: Catechol oxidase                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1bt1B00 B:1-341 Di-copper center containing domain from catechol oxidase                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh........................eee.........eee..hhh..hhhhhhhhhhhhhhh.........hhhhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhh..............hhh....hhhh.................................hhhhhhhhhhhhhhhh......hhhhh...............hhhh..hhhhhhhh................hhh.hhhhhhhhhhhhhhhhhhh..-----.....hhhh..eeeee.....eeeeehhh........eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------TYROSINASE_1      ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1bt1 B   1 APIQAPEISKCVVPPADLPPGAVVDNCCPPVASNIVDYKLPAVTTMKVRPAAHTMDKDAIAKFAKAVELMKALPADDPRNFYQQALVHCAYCNGGYDQVNFPDQEIQVHNSWLFFPFHRWYLYFYERILGKLIGDPSFGLPFWNWDNPGGMVLPDFLNDSTSSLYDSNRNQSHLPPVVVDLGYNGADTDVTDQQRITDNLALMYKQMVTNAGTAELFLGKAYRAGDAPSPGAGSIETSPHIPIHRWVGDPRNTNNEDMGNFYSAGRDIAFYCHHSNVDRMWTIWQQLA-----RDYTDSDWLNATFLFYDENGQAVKVRIGDSLDNQKMGYKYAKTPLPWL 341
                                    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       | -   |   300       310       320       330       340 
                                                                                                                                                                                                                                                                                                                         288   294

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(

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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 alpha proteins (14657)

Fold: Di-copper centre-containing domain (47)

Superfamily: Di-copper centre-containing domain (47)

Family: Catechol oxidase (5)

Protein domain: Catechol oxidase (4)

Sweet potato (Ipomoea batatas) [TaxId: 4120] (4)

1a	d1bt1a_	A:
1b	d1bt1b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: di-copper center containing domain from catechol oxidase (13)

Homologous Superfamily: Di-copper center containing domain from catechol oxidase (13)

Sweet potato (Ipomoea batatas) (4)

1a	1bt1A00	A:1-341
1b	1bt1B00	B:1-341

(no "Pfam Domain" information available for 1BT1)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PPO1_IPOBA | Q9ZP19)

molecular function
	GO:0004097	catechol oxidase activity	Catalysis of the reaction: 2 catechol + O2 = 2 1,2-benzoquinone + 2 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:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0009543	chloroplast thylakoid lumen	The cavity enclosed within the chloroplast thylakoid membrane. An example of this component is found in Arabidopsis thaliana.
	GO:0009536	plastid	Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.
	GO:0009579	thylakoid	A membranous cellular structure that bears the photosynthetic pigments in plants, algae, and cyanobacteria. In cyanobacteria thylakoids are of various shapes and are attached to, or continuous with, the plasma membrane. In eukaryotes they are flattened, membrane-bounded disk-like structures located in the chloroplasts; in the chloroplasts of higher plants the thylakoids form dense stacks called grana. Isolated thylakoid preparations can carry out photosynthetic electron transport and the associated phosphorylation.

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	1.10.3.1
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	PPO1_IPOBA \| Q9ZP19	:	1bt2 1bt3 1bug

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (6, 6)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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