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(-) Description

Title :  D-DOPACHROME TAUTOMERASE (D-DT)/MACROPHAGE MIGRATION INHIBITORY FACTOR 2 (MIF2) COMPLEXED WITH INHIBITOR 4-IPP
 
Authors :  S. Zierow, E. Lolis
Date :  19 Oct 09  (Deposition) - 20 Apr 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.13
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Biol. Unit 3:  C  (3x)
Keywords :  Immune Response, Cytokine, Tautomerase, Cytokine-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Zierow, E. Lolis
Crystal Structure Of D-Dopachrome Tautomerase (D-Dt)/Macrophage Migration Inhibitory Factor 2 (Mif2) Complexed With Inhibitor 4-Ipp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - D-DOPACHROME TAUTOMERASE
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDDT, HCG_41098
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    StrainBL-21
    SynonymD-DOPACHROME TAUTOMERASE, ISOFORM CRA_B, CDNA FLJ76419, HIGHLY SIMILAR TO HOMO SAPIENS D-DOPACHROME TAUTOMERASE (DDT), MRNA

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (3x)A  
Biological Unit 2 (3x) B 
Biological Unit 3 (3x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2RW13Ligand/Ion4-PHENYLPYRIMIDINE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2RW13Ligand/Ion4-PHENYLPYRIMIDINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2RW13Ligand/Ion4-PHENYLPYRIMIDINE
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2RW13Ligand/Ion4-PHENYLPYRIMIDINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:1 , PHE A:2 , ARG A:36 , ASN A:38 , LYS A:109 , MET A:114 , CL A:118 , HOH A:213BINDING SITE FOR RESIDUE RW1 A 120
2AC2SOFTWAREPRO A:1 , LYS A:32 , SER A:63 , ILE A:64 , RW1 A:120 , HOH A:273BINDING SITE FOR RESIDUE CL A 118
3AC3SOFTWAREPRO B:1 , PHE B:2 , ARG B:36 , ASN B:38 , MET B:114 , CL B:118 , HOH B:180BINDING SITE FOR RESIDUE RW1 B 120
4AC4SOFTWAREPRO B:1 , LYS B:32 , SER B:63 , ILE B:64 , RW1 B:120BINDING SITE FOR RESIDUE CL B 118
5AC5SOFTWAREPRO C:1 , PHE C:2 , ARG C:36 , ASN C:38 , MET C:114BINDING SITE FOR RESIDUE RW1 C 120

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KAN)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KAN)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KAN)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIFPS01158 Macrophage migration inhibitory factor family signature.DOPD_HUMAN55-69
 
 
  3A:54-68
B:54-68
C:54-68
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIFPS01158 Macrophage migration inhibitory factor family signature.DOPD_HUMAN55-69
 
 
  3A:54-68
-
-
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIFPS01158 Macrophage migration inhibitory factor family signature.DOPD_HUMAN55-69
 
 
  3-
B:54-68
-
Biological Unit 3 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIFPS01158 Macrophage migration inhibitory factor family signature.DOPD_HUMAN55-69
 
 
  3-
-
C:54-68

(-) Exons   (0, 0)

(no "Exon" information available for 3KAN)

(-) 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: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 d3kana_ A: D-dopachrome tautomerase                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhhheeeee..............eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhhh.ee..ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3kan A   1 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 117
                                    10        20        30        40        50        60        70        80        90       100       110       

Chain A from PDB  Type:PROTEIN  Length:117
 aligned with Q53Y51_HUMAN | Q53Y51 from UniProtKB/TrEMBL  Length:118

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
         Q53Y51_HUMAN     2 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 118
               SCOP domains d3kana_ A: D-dopachrome tautomerase                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhhheeeee..............eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhhh.ee..ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3kan 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 d3kanb_ B: D-dopachrome tautomerase                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhhheeeee..............eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhhh.ee..ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3kan B   1 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 117
                                    10        20        30        40        50        60        70        80        90       100       110       

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with Q53Y51_HUMAN | Q53Y51 from UniProtKB/TrEMBL  Length:118

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
         Q53Y51_HUMAN     2 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 118
               SCOP domains d3kanb_ B: D-dopachrome tautomerase                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhhheeeee..............eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhhh.ee..ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3kan 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 d3kanc_ C: D-dopachrome tautomerase                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) MIF-3kanC01 C:1-115                                                                                                -- Pfam domains (1)
           Pfam domains (2) MIF-3kanC02 C:1-115                                                                                                -- Pfam domains (2)
           Pfam domains (3) MIF-3kanC03 C:1-115                                                                                                -- Pfam domains (3)
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhhheeeee..............eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhhh.ee..ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------MIF            ------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3kan C   1 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 117
                                    10        20        30        40        50        60        70        80        90       100       110       

Chain C from PDB  Type:PROTEIN  Length:117
 aligned with Q53Y51_HUMAN | Q53Y51 from UniProtKB/TrEMBL  Length:118

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
         Q53Y51_HUMAN     2 PFLELDTNLPANRVPAGLEKRLCAAAASILGKPADRVNVTVRPGLAMALSGSTEPCAQLSISSIGVVGTAEDNRSHSAHFFEFLTKELALGQDRILIRFFPLESWQIGKIGTVMTFL 118
               SCOP domains d3kanc_ C: D-dopachrome tautomerase                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) MIF-3kanC01 C:1-115                                                                                                -- Pfam domains (1)
           Pfam domains (2) MIF-3kanC02 C:1-115                                                                                                -- Pfam domains (2)
           Pfam domains (3) MIF-3kanC03 C:1-115                                                                                                -- Pfam domains (3)
         Sec.struct. author .eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhhheeeee..............eeeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeeeehhhh.ee..ee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3kan 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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KAN)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: MIF (36)
(-)
Family: MIF (22)
1aMIF-3kanC01C:1-115
1bMIF-3kanC02C:1-115
1cMIF-3kanC03C:1-115

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q53Y51_HUMAN | Q53Y51)

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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 Related Entries

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

UniProtKB/Swiss-Prot
        DOPD_HUMAN | P300461dpt 4q3f

(-) Related Entries Specified in the PDB File

1dpt D-DOPACHROME TAUTOMERASE
3b64 MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) FROM LEISHMANIA MAJOR
3b9s MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) COMPLEXED WITH INHIBITOR, 4-IPP
3ker D-DOPACHROME TAUTOMERASE (MD-DT)/ MACROPHAGE MIGRATION INHIBITORY FACTOR 2 (MIF2) COMPLEXED WITH INHIBITOR 4-IPP (MUS MUSCULUS)