2P39 - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN FGF23

Authors :   M. Mohammadi

Date :   08 Mar 07 (Deposition) - 10 Apr 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Atypical Beta-Trefoil Fold, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Goetz, A. Beenken, O. A. Ibrahimi, J. Kalinina, S. K. Olsen, A. V. Eliseenkova, C. Xu, T. A. Neubert, F. Zhang, R. J. Linhardt, X. Yu, K. E. White, T. Inagaki, S. A. Kliewer, M. Yamamoto, H. Kurosu, Y. Ogawa, M. Kuro-O, B. Lanske, M. S. Razzaque, M. Mohammadi
Molecular Insights Into The Klotho-Dependent, Endocrine Mode Of Action Of Fibroblast Growth Factor 19 Subfamily Members.
Mol. Cell. Biol. V. 27 3417 2007
PubMed-ID: 17339340 | Reference-DOI: 10.1128/MCB.02249-06
(for further references see the PDB file header)

Molecule 1 - FIBROBLAST GROWTH FACTOR 23
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21 (DE3) PLYS-S
	Expression System Taxid	:	562
	Gene	:	FGF23, HYPF
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	FGF-23, TUMOR-DERIVED HYPOPHOSPHATEMIA-INDUCING FACTOR

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SCR	1	Ligand/Ion	SUCROSE OCTASULFATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:47 , ARG A:48 , ASN A:49 , HIS A:56 , LYS A:57 , ASN A:58 , ARG A:92 , GLY A:139 , ARG A:140 , ALA A:141 , PRO A:147 , GLY A:148 , PRO A:153 , TYR A:154 , HOH A:1014 , HOH A:1016 , HOH A:1018 , HOH A:1037 , HOH A:1043 , HOH A:1071	BINDING SITE FOR RESIDUE SCR A 1

Asymmetric/Biological Unit

No.	Residues
1	A:95	-	A:113

(no "Cis Peptide Bond" information available for 2P39)

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_023831	S	71	G	FGF23_HUMAN	Disease (HFTC)	104894342	A	S	71	G
2	UniProt	VAR_071711	M	96	T	FGF23_HUMAN	Disease (HFTC)	104894343	A	M	96	T
3	UniProt	VAR_071712	S	129	F	FGF23_HUMAN	Disease (HFTC)	104894344	A	S	129	F
4	UniProt	VAR_071713	F	157	L	FGF23_HUMAN	Disease (HFTC)	772964687	A	F	157	L

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2P39)

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000237837	1	ENSE00000802845	chr12:4488894-4488538	357	FGF23_HUMAN	1-71	71	1	A:29-71	43
1.2	ENST00000237837	2	ENSE00000802844	chr12:4481863-4481760	104	FGF23_HUMAN	71-105	35	1	A:71-105	35
1.3	ENST00000237837	3	ENSE00000997496	chr12:4479949-4477393	2557	FGF23_HUMAN	106-251	146	1	A:106-170	65

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
	(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:142
 aligned with FGF23_HUMAN | Q9GZV9 from UniProtKB/Swiss-Prot  Length:251

    Alignment length:142
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168  
          FGF23_HUMAN    29 SPLLGSSWGGLIHLYTATARNSYHLQIHKNGHVDGAPHQTIYSALMIRSEDAGFVVITGVMSRRYLCMDFRGNIFGSHYFDPENCRFQHQTLENGYDVYHSPQYHFLVSLGRAKRAFLPGMNPPPYSQFLSRRNEIPLIHFN 170
               SCOP domains d2p39a_ A: automated matches                                                                                                                   SCOP domains
               CATH domains 2p39A00 A:29-170  [code=2.80.10.50, no name defined]                                                                                           CATH domains
               Pfam domains ----------FGF-2p39A01 A:39-147                                                                                         ----------------------- Pfam domains
         Sec.struct. author ...........eeee........eeee.....eeee........eeeee....eeeeee....eeeee.....eeee.........eeeee.....eeee.......................hhhhh.eeee...hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------G------------------------T--------------------------------F---------------------------L------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:29-71 UniProt: 1-71       ----------------------------------Exon 1.3  PDB: A:106-170 UniProt: 106-251 [INCOMPLETE]            Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.2  PDB: A:71-105            ----------------------------------------------------------------- Transcript 1 (2)
                 2p39 A  29 SPLLGSSWGGLIHLYTATARNSYHLQIHKNGHVDGAPHQTIYSALMIRSEDAGFVVITGVMSRRYLCMDFRGNIFGSHYFDPENCRFQHQTLENGYDVYHSPQYHFLVSLGRAKRAFLPGMNPPPYSQFLSRRNEIPLIHFN 170
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-Trefoil (385)

Superfamily: Cytokine (169)

Family: automated matches (5)

Protein domain: automated matches (5)

Human (Homo sapiens) [TaxId: 9606] (4)

d2p39a_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Trefoil (289)

Topology: Trefoil (Acidic Fibroblast Growth Factor, subunit A) (289)

Homologous Superfamily: [code=2.80.10.50, no name defined] (289)

Human (Homo sapiens) (131)

2p39A00

A:29-170

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Trefoil (131)

Family: FGF (36)

Homo sapiens (Human) (34)

FGF-2p39A01

A:39-147

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (FGF23_HUMAN | Q9GZV9)

molecular function
	GO:0016303	1-phosphatidylinositol-3-kinase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol + ATP = a 1-phosphatidyl-1D-myo-inositol 3-phosphate + ADP + 2 H(+).
	GO:0005088	Ras guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0005104	fibroblast growth factor receptor binding	Interacting selectively and non-covalently with the fibroblast growth factor receptor (FGFR).
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0046934	phosphatidylinositol-4,5-bisphosphate 3-kinase activity	Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
	GO:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	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.
	GO:0005105	type 1 fibroblast growth factor receptor binding	Interacting selectively and non-covalently with the type 1 fibroblast growth factor receptor (FGFR1).
biological process
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0030643	cellular phosphate ion homeostasis	Any process involved in the maintenance of an internal steady state of phosphate ions at the level of a cell.
	GO:0071354	cellular response to interleukin-6	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an interleukin-6 stimulus.
	GO:0044320	cellular response to leptin stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a leptin stimulus. Leptin is a hormone manufactured primarily in the adipocytes of white adipose tissue, and the level of circulating leptin is directly proportional to the total amount of fat in the body. It plays a key role in regulating energy intake and energy expenditure, including appetite and metabolism.
	GO:0071374	cellular response to parathyroid hormone stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a parathyroid hormone stimulus.
	GO:0071305	cellular response to vitamin D	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin D stimulus.
	GO:0008543	fibroblast growth factor receptor signaling pathway	The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
	GO:0030502	negative regulation of bone mineralization	Any process that stops, prevents, or reduces the frequency, rate or extent of bone mineralization.
	GO:0046888	negative regulation of hormone secretion	Any process that stops, prevents, or reduces the frequency, rate or extent of the regulated release of a hormone from a cell.
	GO:0045668	negative regulation of osteoblast differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of osteoblast differentiation.
	GO:0018108	peptidyl-tyrosine phosphorylation	The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
	GO:0055062	phosphate ion homeostasis	Any process involved in the maintenance of an internal steady state of phosphate ions within an organism or cell.
	GO:0006796	phosphate-containing compound metabolic process	The chemical reactions and pathways involving the phosphate group, the anion or salt of any phosphoric acid.
	GO:0046854	phosphatidylinositol phosphorylation	The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
	GO:0036092	phosphatidylinositol-3-phosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of phosphatidylinositol-3-phosphate, a phosphatidylinositol monophosphate carrying the phosphate group at the 3-position.
	GO:0048015	phosphatidylinositol-mediated signaling	A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
	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:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0090080	positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway	The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands resulting in an increase in the rate or frequency of a MAPKKK cascade.
	GO:0045893	positive regulation of transcription, DNA-templated	Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0010980	positive regulation of vitamin D 24-hydroxylase activity	Any process that increases the rate, frequency or extent of vitamin D 24-hydroxylase activity. Vitamin D 24-hydroxylase activity catalyzes the hydroxylation of C-24 of any form of vitamin D.
	GO:0030500	regulation of bone mineralization	Any process that modulates the frequency, rate or extent of bone mineralization.
	GO:0010966	regulation of phosphate transport	Any process that modulates the frequency, rate or extent of phosphate transport. Phosphate transport is the directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0014066	regulation of phosphatidylinositol 3-kinase signaling	Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0032026	response to magnesium ion	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a magnesium ion stimulus.
	GO:1904383	response to sodium phosphate	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a sodium phosphate stimulus.
	GO:0042369	vitamin D catabolic process	The chemical reactions and pathways resulting in the breakdown of vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
	GO:0042359	vitamin D metabolic process	The chemical reactions and pathways involving vitamin D, any of a group of related, fat-soluble compounds that are derived from delta-5,7 steroids and play a central role in calcium metabolism. Specific forms of vitamin D include calciferol (ergocalciferol; vitamin D2) and cholecalciferol (calciol; vitamin D3).
cellular component
	GO:0005796	Golgi lumen	The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.
	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.

Asymmetric/Biological Unit
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2p23	CRYSTAL STRUCTURE OF HUMAN FGF19

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (0, 0)

Exons (3, 3)

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SCOP Domains (1, 1)

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