1DPT - JenaLib

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Title :   D-DOPACHROME TAUTOMERASE

Authors :   H. Sugimoto, M. Taniguchi, A. Nakagawa, I. Tanaka

Date :   11 May 98 (Deposition) - 30 Mar 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.54

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: B  (3x)
Biol. Unit 5: C  (3x)

Keywords :   Cytokine, Growth Factor, Tautomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Sugimoto, M. Taniguchi, A. Nakagawa, I. Tanaka, M. Suzuki, J. Nishihira
Crystal Structure Of Human D-Dopachrome Tautomerase, A Homologue Of Macrophage Migration Inhibitory Factor, At 1. 5 A Resolution.
Biochemistry V. 38 3268 1999
PubMed-ID: 10079069 | Reference-DOI: 10.1021/BI982184O
(for further references see the PDB file header)

Molecule 1 - D-DOPACHROME TAUTOMERASE
	Cell Line	:	BL21
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3
	Expression System Strain	:	BL21 (DE3) LYSS
	Expression System Taxid	:	562
	Organ	:	LIVER
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (3x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (3x)	:		B
Biological Unit 5 (3x)	:			C

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1DPT)

(no "Site" information available for 1DPT)

(no "SS Bond" information available for 1DPT)

(no "Cis Peptide Bond" information available for 1DPT)

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIF	PS01158	Macrophage migration inhibitory factor family signature.	DOPD_HUMAN	55-69	3	A:54-68 B:54-68 C:54-68

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIF	PS01158	Macrophage migration inhibitory factor family signature.	DOPD_HUMAN	55-69	3	A:54-68 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIF	PS01158	Macrophage migration inhibitory factor family signature.	DOPD_HUMAN	55-69	1	- B:54-68 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIF	PS01158	Macrophage migration inhibitory factor family signature.	DOPD_HUMAN	55-69	1	- - C:54-68

Biological Unit 4 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIF	PS01158	Macrophage migration inhibitory factor family signature.	DOPD_HUMAN	55-69	3	- B:54-68 -

Biological Unit 5 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MIF	PS01158	Macrophage migration inhibitory factor family signature.	DOPD_HUMAN	55-69	3	- - C:54-68

Asymmetric Unit (3, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.4a	ENST00000398344	4a	ENSE00001895724	chr22:24316773-24316496	278	DOPD_HUMAN	1-36	36	3	A:1-35 B:1-35 C:1-35	35 35 35
1.5a	ENST00000398344	5a	ENSE00001664306	chr22:24316132-24315957	176	DOPD_HUMAN	37-95	59	3	A:36-94 B:36-94 C:36-94	59 59 59
1.6c	ENST00000398344	6c	ENSE00001552489	chr22:24313812-24313554	259	DOPD_HUMAN	95-118	24	3	A:94-117 B:94-117 C:94-117	24 24 24

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:117
 aligned with DOPD_HUMAN | P30046 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           DOPD_HUMAN     2 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 118
               SCOP domains d1dpta_ A: D-dopachrome tautomerase                                                                                   SCOP domains
               CATH domains 1dptA00 A:1-117 Macrophage Migration Inhibitory Factor                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhh....hhhhhhhhhhhhh...hhh.eeeee..............eeeeeeee.....hhhhhhhhhhhhhhhhhhh...hhheeeeeeee.hhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: A:1-35 [INCOMPLETE]Exon 1.5a  PDB: A:36-94 UniProt: 37-95                     ----------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------Exon 1.6c  PDB: A:94-117 Transcript 1 (2)
                 1dpt A   1 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with DOPD_HUMAN | P30046 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           DOPD_HUMAN     2 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 118
               SCOP domains d1dptb_ B: D-dopachrome tautomerase                                                                                   SCOP domains
               CATH domains 1dptB00 B:1-117 Macrophage Migration Inhibitory Factor                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhh....hhhhhhhhhhhhh...hhh.eeeee..............eeeeeeee.....hhhhhhhhhhhhhhhhhhh...hhheeeeeeee.hhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: B:1-35 [INCOMPLETE]Exon 1.5a  PDB: B:36-94 UniProt: 37-95                     ----------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------Exon 1.6c  PDB: B:94-117 Transcript 1 (2)
                 1dpt B   1 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:117
 aligned with DOPD_HUMAN | P30046 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           DOPD_HUMAN     2 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 118
               SCOP domains d1dptc_ C: D-dopachrome tautomerase                                                                                   SCOP domains
               CATH domains 1dptC00 C:1-117 Macrophage Migration Inhibitory Factor                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhh....hhhhhhhhhhhhh...hhh.eeeee..............eeeeeeee.....hhhhhhhhhhhhhhhhhhh...hhheeeeeeee.hhh........... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  PDB: C:1-35 [INCOMPLETE]Exon 1.5a  PDB: C:36-94 UniProt: 37-95                     ----------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------Exon 1.6c  PDB: C:94-117 Transcript 1 (2)
                 1dpt C   1 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 117
                                    10        20        30        40        50        60        70        80        90       100       110

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: Alpha and beta proteins (a+b) (23004)

Fold: Tautomerase/MIF (104)

Superfamily: Tautomerase/MIF (104)

Family: MIF-related (58)

Protein domain: D-dopachrome tautomerase (2)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d1dpta_	A:
1b	d1dptb_	B:
1c	d1dptc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Macrophage Migration Inhibitory Factor (40)

Homologous Superfamily: Macrophage Migration Inhibitory Factor (40)

Human (Homo sapiens) (25)

1a	1dptA00	A:1-117
1b	1dptB00	B:1-117
1c	1dptC00	C:1-117

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

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DOPD_HUMAN | P30046)

molecular function
	GO:0033981	D-dopachrome decarboxylase activity	Catalysis of the reaction: D-dopachrome + H(+) = 5,6-dihydroxyindole + CO(2).
	GO:0004167	dopachrome isomerase activity	Catalysis of the reaction: L-dopachrome = 5,6-dihydroxyindole-2-carboxylate.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0042438	melanin biosynthetic process	The chemical reactions and pathways resulting in the formation of melanins, pigments largely of animal origin. High molecular weight polymers of indole quinone, they are irregular polymeric structures and are divided into three groups: allomelanins in the plant kingdom and eumelanins and phaeomelanins in the animal kingdom.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

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