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Title :   CRYSTAL STRUCTURE OF MACROPHAGE MIGRATION INHIBITORY FACTOR (MIF) WITH IMIDAZOPYRIDAZINOL INHIBITOR AT 1.80A RESOLUTION

Authors :   L. Mclean, Y. Zhang

Date :   22 Dec 09 (Deposition) - 09 Mar 10 (Release) - 09 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Protein-Ligand Complex, Cytokine, Cytoplasm, Immune Response, Inflammatory Response, Innate Immunity, Isomerase, Phosphoprotein, Secreted, Acetylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. R. Mclean, Y. Zhang, H. Li, Y. M. Choi, Z. Han, R. J. Vaz, Y. Li
Fragment Screening Of Inhibitors For Mif Tautomerase Reveals A Cryptic Surface Binding Site.
Bioorg. Med. Chem. Lett. V. 20 1821 2010
PubMed-ID: 20185308 | Reference-DOI: 10.1016/J.BMCL.2010.02.009

Molecule 1 - MACROPHAGE MIGRATION INHIBITORY FACTOR
	Chains	:	A, B, C
	EC Number	:	5.3.2.1, 5.3.3.12
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLIF, MIF, MMIF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MIF, PHENYLPYRUVATE TAUTOMERASE, L-DOPACHROME TAUTOMERASE, L-DOPACHROME ISOMERASE, GLYCOSYLATION- INHIBITING FACTOR, GIF

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	428	1	Ligand/Ion	2-(1-METHYLETHYL)IMIDAZO[1,2-B]PYRIDAZIN-6-OL
2	GOL	3	Ligand/Ion	GLYCEROL
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:35 , TYR A:36 , TRP A:108 , PHE A:113 , GOL A:124 , HOH A:127 , HOH A:181 , GLU B:54 , TYR C:95	BINDING SITE FOR RESIDUE 428 A 123
2	AC2	SOFTWARE	PRO A:1 , MET A:2 , HIS A:62 , SER A:63 , 428 A:123 , HOH A:181 , TYR C:95 , ASN C:97	BINDING SITE FOR RESIDUE GOL A 124
3	AC3	SOFTWARE	ASN A:97 , PRO B:1 , MET B:2 , HIS B:62 , SER B:63 , ILE B:64 , VAL B:106 , HOH B:188	BINDING SITE FOR RESIDUE GOL B 123
4	AC4	SOFTWARE	ARG A:11 , HIS B:117	BINDING SITE FOR RESIDUE SO4 B 124
5	AC5	SOFTWARE	TYR B:95 , ASN B:97 , HOH B:233 , PRO C:1 , MET C:2 , HIS C:62 , SER C:63 , HOH C:147	BINDING SITE FOR RESIDUE GOL C 123
6	AC6	SOFTWARE	ARG B:11 , HIS C:117 , HIS C:118	BINDING SITE FOR RESIDUE SO4 C 124

(no "SS Bond" information available for 3L5P)

(no "Cis Peptide Bond" information available for 3L5P)

(no "SAP(SNP)/Variant" information available for 3L5P)

Asymmetric/Biological Unit (1, 3)

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

Asymmetric/Biological Unit (3, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000215754	1a	ENSE00001922200	chr22:24236191-24236769	579	MIF_HUMAN	1-36	36	3	A:1-35 B:1-35 C:1-35	35 35 35
1.2b	ENST00000215754	2b	ENSE00000651496	chr22:24236959-24237131	173	MIF_HUMAN	37-94	58	3	A:36-93 B:36-93 C:36-93	58 58 58
1.2d	ENST00000215754	2d	ENSE00001839840	chr22:24237227-24237413	187	MIF_HUMAN	94-115	22	3	A:93-114 B:93-114 C:93-114	22 22 22

Asymmetric/Biological 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:114
 aligned with MIF_HUMAN | P14174 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:114
                                    11        21        31        41        51        61        71        81        91       101       111    
            MIF_HUMAN     2 PMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLRISPDRVYINYYDMNAANVGWNNSTFA 115
               SCOP domains d3l5pa_ A: Microphage migration inhibition factor (MIF)                                                            SCOP domains
               CATH domains 3l5pA00 A:1-114 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 1 (1) Exon 1.1a  PDB: A:1-35 [INCOMPLETE]Exon 1.2b  PDB: A:36-93 UniProt: 37-94                    --------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------Exon 1.2d              Transcript 1 (2)
                 3l5p A   1 PMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLRISPDRVYINYYDMNAANVGWNNSTFA 114
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with MIF_HUMAN | P14174 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:117
                                                                                                                                           115   
                                    11        21        31        41        51        61        71        81        91       101       111   |   
            MIF_HUMAN     2 PMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLRISPDRVYINYYDMNAANVGWNNSTFA---   -
               SCOP domains d3l5pb_ B: Microphage migration inhibition factor (MIF)                                                               SCOP domains
               CATH domains 3l5pB00 B:1-117 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 1 (1) Exon 1.1a  PDB: B:1-35 [INCOMPLETE]Exon 1.2b  PDB: B:36-93 UniProt: 37-94                    ------------------------ Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------Exon 1.2d             --- Transcript 1 (2)
                 3l5p B   1 PMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLRISPDRVYINYYDMNAANVGWNNSTFALEH 117
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:118
 aligned with MIF_HUMAN | P14174 from UniProtKB/Swiss-Prot  Length:115

    Alignment length:118
                                                                                                                                           115    
                                    11        21        31        41        51        61        71        81        91       101       111   |    
            MIF_HUMAN     2 PMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLRISPDRVYINYYDMNAANVGWNNSTFA----   -
               SCOP domains d3l5pc_ C: Microphage migration inhibition factor (MIF)                                                                SCOP domains
               CATH domains 3l5pC00 C:1-118 Macrophage Migration Inhibitory Factor                                                                 CATH domains
           Pfam domains (1) MIF-3l5pC01 C:1-114                                                                                               ---- Pfam domains (1)
           Pfam domains (2) MIF-3l5pC02 C:1-114                                                                                               ---- Pfam domains (2)
           Pfam domains (3) MIF-3l5pC03 C:1-114                                                                                               ---- Pfam domains (3)
         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 1 (1) Exon 1.1a  PDB: C:1-35 [INCOMPLETE]Exon 1.2b  PDB: C:36-93 UniProt: 37-94                    ------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------Exon 1.2d             ---- Transcript 1 (2)
                 3l5p C   1 PMFIVNTNVPRASVPDGFLSELTQQLAQATGKPPQYIAVHVVPDQLMAFGGSSEPCALCSLHSIGKIGGAQNRSYSKLLCGLLAERLRISPDRVYINYYDMNAANVGWNNSTFALEHH 118
                                    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/Biological 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( (-)

)

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

Fold: Tautomerase/MIF (104)

Superfamily: Tautomerase/MIF (104)

Family: MIF-related (58)

Protein domain: Microphage migration inhibition factor (MIF) (55)

Human (Homo sapiens) [TaxId: 9606] (46)

1a	d3l5pa_	A:
1b	d3l5pb_	B:
1c	d3l5pc_	C:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

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	3l5pB00	B:1-117
1b	3l5pC00	C:1-118
1c	3l5pA00	A:1-114

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MIF (36)

Family: MIF (22)

Homo sapiens (Human) (16)

1a	MIF-3l5pC01	C:1-114
1b	MIF-3l5pC02	C:1-114
1c	MIF-3l5pC03	C:1-114

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (MIF_HUMAN | P14174)

molecular function
	GO:0042056	chemoattractant activity	Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
	GO:0005125	cytokine activity	Functions to control the survival, growth, differentiation and effector function of tissues and cells.
	GO:0005126	cytokine receptor binding	Interacting selectively and non-covalently with a cytokine receptor.
	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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
biological process
	GO:0030330	DNA damage response, signal transduction by p53 class mediator	A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
	GO:0019752	carboxylic acid metabolic process	The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
	GO:0007569	cell aging	An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0007166	cell surface receptor signaling pathway	A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
	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.
	GO:0050900	leukocyte migration	The movement of a leukocyte within or between different tissues and organs of the body.
	GO:0043518	negative regulation of DNA damage response, signal transduction by p53 class mediator	Any process that stops, prevents, or reduces the frequency, rate or extent of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0090344	negative regulation of cell aging	Any process that decreases the rate, frequency, or extent of cell aging. Cell aging is the progression of the cell from its inception to the end of its lifespan.
	GO:0071157	negative regulation of cell cycle arrest	Any process that decreases the rate, frequency, or extent of cell cycle arrest, the process in which the cell cycle is halted during one of the normal phases.
	GO:0032269	negative regulation of cellular protein metabolic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways involving a protein, occurring at the level of an individual cell.
	GO:0010629	negative regulation of gene expression	Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:1902166	negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator	Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator.
	GO:0002906	negative regulation of mature B cell apoptotic process	Any process that stops, prevents, or reduces the frequency, rate, or extent of mature B cell apoptotic process.
	GO:0033033	negative regulation of myeloid cell apoptotic process	Any process that stops, prevents, or reduces the frequency, rate, or extent of a myeloid cell apoptotic process.
	GO:0050918	positive chemotaxis	The directed movement of a motile cell or organism towards a higher concentration of a chemical.
	GO:0030890	positive regulation of B cell proliferation	Any process that activates or increases the rate or extent of B cell proliferation.
	GO:0070374	positive regulation of ERK1 and ERK2 cascade	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
	GO:0043406	positive regulation of MAP kinase activity	Any process that activates or increases the frequency, rate or extent of MAP kinase activity.
	GO:0090238	positive regulation of arachidonic acid secretion	Any process that increases the rate, frequency, or extent of arachidonic acid secretion, the controlled release of arachidonic acid from a cell or a tissue.
	GO:2000343	positive regulation of chemokine (C-X-C motif) ligand 2 production	Any process that activates or increases the frequency, rate or extent of chemokine (C-X-C motif) ligand 2 production.
	GO:0050715	positive regulation of cytokine secretion	Any process that activates or increases the frequency, rate or extent of the regulated release of cytokines from a cell.
	GO:0048146	positive regulation of fibroblast proliferation	Any process that activates or increases the frequency, rate or extent of multiplication or reproduction of fibroblast cells.
	GO:0031666	positive regulation of lipopolysaccharide-mediated signaling pathway	Any process that activates or increases the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
	GO:0061081	positive regulation of myeloid leukocyte cytokine production involved in immune response	Any process that modulates the rate, frequency, or extent of the production of a cytokine that contributes to the immune response.
	GO:0033138	positive regulation of peptidyl-serine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0042327	positive regulation of phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
	GO:0061078	positive regulation of prostaglandin secretion involved in immune response	Any process that activates or increases the frequency, rate or extent of the regulated release of a prostaglandin from a cell and contributes to the immune response.
	GO:0010739	positive regulation of protein kinase A signaling	Any process that increases the rate, frequency, or extent of protein kinase A signaling. PKA signaling is the series of reactions, mediated by the intracellular serine/threonine kinase protein kinase A, which occurs as a result of a single trigger reaction or compound.
	GO:0001934	positive regulation of protein phosphorylation	Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
	GO:0001516	prostaglandin biosynthetic process	The chemical reactions and pathways resulting in the formation of prostaglandins, any of a group of biologically active metabolites which contain a cyclopentane ring.
	GO:0070207	protein homotrimerization	The formation of a protein homotrimer, a macromolecular structure consisting of three noncovalently associated identical subunits.
	GO:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0043030	regulation of macrophage activation	Any process that modulates the frequency or rate of macrophage activation.
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	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.
	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.
	GO:0043209	myelin sheath	An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	GO:0031982	vesicle	Any small, fluid-filled, spherical organelle enclosed by membrane.

Asymmetric/Biological Unit
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	3l5p
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

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Exons (3, 9)

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