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(-) Description

Title :  CRYSTAL STRUCTURE OF MACROPHAGE MIGRATION INHIBITORY FACTOR FROM XENOPUS LAEVIS.
 
Authors :  M. Suzuki, Y. Takamura, M. Maeno, S. Tochinai, D. Iyaguchi, I. Tanaka, J. Nishihira, T. Ishibashi
Date :  24 Jul 03  (Deposition) - 25 May 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D  (3x)
Keywords :  Cytokine, Tautomerase, Macrophage Migration Inhibitory Factor, Mif (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Suzuki, Y. Takamura, M. Maeno, S. Tochinai, D. Iyaguchi, I. Tanaka, J. Nishihira, T. Ishibashi
Xenopus Laevis Macrophage Migration Inhibitory Factor Is Essential For Axis Formation And Neural Development.
J. Biol. Chem. V. 279 21406 2004
PubMed-ID: 15024012  |  Reference-DOI: 10.1074/JBC.M311416200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MACROPHAGE MIGRATION INHIBITORY FACTOR
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: MIF

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABC 
Biological Unit 2 (3x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

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

(-) Sites  (0, 0)

(no "Site" information available for 1UIZ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIFPS01158 Macrophage migration inhibitory factor family signature.MIF_XENLA55-69
 
 
 		  4A:54-68
B:54-68
C:54-68
D:54-68
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIFPS01158 Macrophage migration inhibitory factor family signature.MIF_XENLA55-69
 
 
 		  3A:54-68
B:54-68
C:54-68
-
Biological Unit 2 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MIFPS01158 Macrophage migration inhibitory factor family signature.MIF_XENLA55-69
 
 
 		  3-
-
-
D:54-68

(-) Exons   (0, 0)

(no "Exon" information available for 1UIZ)

(-) 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:115
 aligned with MIF_XENLA | Q76BK2 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:115
                                    10        20        30        40        50        60        70        80        90       100       110     
            MIF_XENLA     1 MPVFTIRTNVCRDSVPDTLLSDLTKQLAKATGKPAEYIAIHIVPDQIMSFGDSTDPCAVCSLCSIGKIGGPQNKSYTKLLCDILTKQLNIPANRVYINYYDLNAANVGWNGSTFA 115
               SCOP domains d1uiza_ A: Microphage migration inhibition factor (MIF)                                                             SCOP domains
               CATH domains 1uizA00 A:0-114 Macrophage Migration Inhibitory Factor                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhh.eeeee...eeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------MIF            ---------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1uiz A   0 MPVFTIRTNVCRDSVPDTLLSDLTKQLAKATGKPAEYIAIHIVPDQIMSFGDSTDPCAVCSLCSIGKIGGPQNKSYTKLLCDILTKQLNIPANRVYINYYDLNAANVGWNGSTFA 114
                                     9        19        29        39        49        59        69        79        89        99       109     


Chain B from PDB  Type:PROTEIN  Length:115
 aligned with MIF_XENLA | Q76BK2 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:115
                                    10        20        30        40        50        60        70        80        90       100       110     
            MIF_XENLA     1 MPVFTIRTNVCRDSVPDTLLSDLTKQLAKATGKPAEYIAIHIVPDQIMSFGDSTDPCAVCSLCSIGKIGGPQNKSYTKLLCDILTKQLNIPANRVYINYYDLNAANVGWNGSTFA 115
               SCOP domains d1uizb_ B: Microphage migration inhibition factor (MIF)                                                             SCOP domains
               CATH domains 1uizB00 B:0-114 Macrophage Migration Inhibitory Factor                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhh.eeeee...eeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------MIF            ---------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1uiz B   0 MPVFTIRTNVCRDSVPDTLLSDLTKQLAKATGKPAEYIAIHIVPDQIMSFGDSTDPCAVCSLCSIGKIGGPQNKSYTKLLCDILTKQLNIPANRVYINYYDLNAANVGWNGSTFA 114
                                     9        19        29        39        49        59        69        79        89        99       109     


Chain C from PDB  Type:PROTEIN  Length:115
 aligned with MIF_XENLA | Q76BK2 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:115
                                    10        20        30        40        50        60        70        80        90       100       110     
            MIF_XENLA     1 MPVFTIRTNVCRDSVPDTLLSDLTKQLAKATGKPAEYIAIHIVPDQIMSFGDSTDPCAVCSLCSIGKIGGPQNKSYTKLLCDILTKQLNIPANRVYINYYDLNAANVGWNGSTFA 115
               SCOP domains d1uizc_ C: Microphage migration inhibition factor (MIF)                                                             SCOP domains
               CATH domains 1uizC00 C:0-114 Macrophage Migration Inhibitory Factor                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhh.eeeee...eeee.......eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.eee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------MIF            ---------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1uiz C   0 MPVFTIRTNVCRDSVPDTLLSDLTKQLAKATGKPAEYIAIHIVPDQIMSFGDSTDPCAVCSLCSIGKIGGPQNKSYTKLLCDILTKQLNIPANRVYINYYDLNAANVGWNGSTFA 114
                                     9        19        29        39        49        59        69        79        89        99       109     


Chain D from PDB  Type:PROTEIN  Length:115
 aligned with MIF_XENLA | Q76BK2 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:115
                                    10        20        30        40        50        60        70        80        90       100       110     
            MIF_XENLA     1 MPVFTIRTNVCRDSVPDTLLSDLTKQLAKATGKPAEYIAIHIVPDQIMSFGDSTDPCAVCSLCSIGKIGGPQNKSYTKLLCDILTKQLNIPANRVYINYYDLNAANVGWNGSTFA 115
               SCOP domains d1uizd_ D: Microphage migration inhibition factor (MIF)                                                             SCOP domains
               CATH domains 1uizD00 D:0-114 Macrophage Migration Inhibitory Factor                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..hhhhh..hhhhhhhhhhhhhhh.hhhhheeeee..............eeeeeee....hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhhh.ee..ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------MIF            ---------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1uiz D   0 MPVFTIRTNVCRDSVPDTLLSDLTKQLAKATGKPAEYIAIHIVPDQIMSFGDSTDPCAVCSLCSIGKIGGPQNKSYTKLLCDILTKQLNIPANRVYINYYDLNAANVGWNGSTFA 114
                                     9        19        29        39        49        59        69        79        89        99       109
   Legend:   → Mismatch (orange background)
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  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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MIF_XENLA | Q76BK2)
molecular function
    GO:0005125    cytokine activity    Functions to control the survival, growth, differentiation and effector function of tissues and cells.
    GO:0004167    dopachrome isomerase activity    Catalysis of the reaction: L-dopachrome = 5,6-dihydroxyindole-2-carboxylate.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0050178    phenylpyruvate tautomerase activity    Catalysis of the reaction: keto-phenylpyruvate = enol-phenylpyruvate.
biological process
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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