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Title :   CRYSTAL STRUCTURE OF THE D100E MUTANT OF THE INDIAN HEDGEHOG N-TERMINAL SIGNALLING DOMAIN

Authors :   Y. -X. He, Y. Kang, W. J. Zhang, J. Yu, G. Ma, C. -Z. Zhou

Date :   13 Oct 09 (Deposition) - 26 Jan 11 (Release) - 26 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : B

Keywords :   Alpha+Beta Sandwich, Autocatalytic Cleavage, Cell Membrane, Developmental Protein, Disease Mutation, Glycoprotein, Hydrolase, Lipoprotein, Membrane, Palmitate, Protease, Secreted, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. -X. He, Y. Kang, W. J. Zhang, J. Yu, G. Ma, C. -Z. Zhou
Crystal Structure Of The D100E Mutant Of The Indian Hedgeho N-Terminal Signalling Domain
To Be Published
PubMed: search

Molecule 1 - INDIAN HEDGEHOG PROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	ROSSETA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	INDIAN HEDGEHOG PROTEIN N-PRODUCT
	Gene	:	IHH
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	IHH, HHG-2

		1
Asymmetric/Biological Unit	:	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CO3	1	Ligand/Ion	CARBONATE ION
2	SO4	5	Ligand/Ion	SULFATE ION
3	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS B:145 , ASP B:152 , HIS B:187 , CO3 B:203 , HOH B:295	BINDING SITE FOR RESIDUE ZN B 1001
2	AC2	SOFTWARE	GLN B:51 , SER B:53 , ARG B:168	BINDING SITE FOR RESIDUE SO4 B 1
3	AC3	SOFTWARE	TYR B:67 , GLY B:69 , LYS B:70 , ARG B:160	BINDING SITE FOR RESIDUE SO4 B 2
4	AC4	SOFTWARE	HOH B:14 , ARG B:66 , LYS B:92 , ARG B:128 , ARG B:158 , HOH B:221 , HOH B:270	BINDING SITE FOR RESIDUE SO4 B 3
5	AC5	SOFTWARE	LYS B:92 , GLN B:105 , LYS B:108 , ARG B:128 , ARG B:158 , HOH B:207 , HOH B:214 , HOH B:229 , HOH B:270	BINDING SITE FOR RESIDUE SO4 B 6
6	AC6	SOFTWARE	THR B:60 , LEU B:61 , ARG B:66 , LYS B:92 , HOH B:278	BINDING SITE FOR RESIDUE SO4 B 7
7	AC7	SOFTWARE	HOH B:11 , HIS B:139 , SER B:140 , SER B:143 , HIS B:145 , GLU B:181 , HOH B:258 , HOH B:295 , ZN B:1001	BINDING SITE FOR RESIDUE CO3 B 203

(no "SS Bond" information available for 3K7J)

Asymmetric/Biological Unit

No.	Residues
1	Ser B:53	-	Pro B:54

Asymmetric/Biological Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_015981	P	46	L	IHH_HUMAN	Disease (ACFD)	121917856	B	P	46	L
2	UniProt	VAR_015983	D	100	E	IHH_HUMAN	Disease (BDA1)	121917854	B	E	100	E
3	UniProt	VAR_015984	D	100	N	IHH_HUMAN	Disease (BDA1)	28936377	B	E	100	N
4	UniProt	VAR_015985	E	131	K	IHH_HUMAN	Disease (BDA1)	121917853	B	E	131	K
5	UniProt	VAR_015986	V	190	A	IHH_HUMAN	Disease (ACFD)	121917857	B	V	190	A

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

(no "PROSITE Motif" information available for 3K7J)

(no "Exon" information available for 3K7J)

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 B from PDB  Type:PROTEIN  Length:146
 aligned with IHH_HUMAN | Q14623 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:152
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190  
            IHH_HUMAN    41 PRKLVPLAYKQFSPNVPEKTLGASGRYEGKIARSSERFKELTPNYNPDIIFKDEENTGADRLMTQRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKS 192
               SCOP domains d3k7jb_ B: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains HH_signal-3k7jB01 B:41-189                                                                                                                           --- Pfam domains
         Sec.struct. author ...........ee......................hhhhhhee.....eee.------...eehhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhh.eeeeee...hhhhhhhhhhhhhhh...eeeeee..eeeee... Sec.struct. author
             SAPs(SNPs) (1) -----L-----------------------------------------------------E------------------------------K----------------------------------------------------------A-- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------N-------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3k7j B  41 PRKLVPLAYKQFSPNVPEKTLGASGRYEGKIARSSERFKELTPNYNPDIIFK------AERLMTQRCKDRLNSLAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGRAVDITTSDRDRNKYGLLARLAVEAGFDWVYYESKAHVHCSVKS 192
                                    50        60        70        80        90 |     100       110       120       130       140       150       160       170       180       190  
                                                                              92     99

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

Fold: Hedgehog/DD-peptidase (29)

Superfamily: Hedgehog/DD-peptidase (29)

Family: Hedgehog (development protein), N-terminal signaling domain (23)

Protein domain: automated matches (18)

Human (Homo sapiens) [TaxId: 9606] (16)

d3k7jb_

(no "CATH Domain" information available for 3K7J)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_MD (20)

Family: HH_signal (16)

Homo sapiens (Human) (13)

HH_signal-3k7jB01

B:41-189

Asymmetric/Biological Unit(hide GO term definitions)

Chain B (IHH_HUMAN | Q14623)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0005113	patched binding	Interacting selectively and non-covalently with the patched (ptc) protein, a receptor for hedgehog proteins.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0051216	cartilage development	The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
	GO:0007267	cell-cell signaling	Any process that mediates the transfer of information from one cell to another. This process includes signal transduction in the receiving cell and, where applicable, release of a ligand and any processes that actively facilitate its transport and presentation to the receiving cell. Examples include signaling via soluble ligands, via cell adhesion molecules and via gap junctions.
	GO:0042733	embryonic digit morphogenesis	The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.
	GO:0001947	heart looping	The tube morphogenesis process in which the primitive heart tube loops asymmetrically. This looping brings the primitive heart chambers into alignment preceding their future integration. Heart looping begins with dextral-looping and ends when the main regional divisions of the mature heart and primordium of the great arterial trunks become established preceeding septation.
	GO:0016539	intein-mediated protein splicing	The removal of an internal amino acid sequence (an intein) from a protein during protein maturation; the excision of inteins is precise and the N- and C-terminal exteins are joined by a normal peptide bond. Protein splicing involves 4 nucleophilic displacements by the 3 conserved splice junction residues.
	GO:0060135	maternal process involved in female pregnancy	A reproductive process occurring in the mother that allows an embryo or fetus to develop within it.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0033085	negative regulation of T cell differentiation in thymus	Any process that stops, prevents, or reduces the frequency, rate or extent of T cell differentiation in the thymus.
	GO:0046639	negative regulation of alpha-beta T cell differentiation	Any process that stops, prevents, or reduces the frequency, rate or extent of alpha-beta T cell differentiation.
	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:0033088	negative regulation of immature T cell proliferation in thymus	Any process that stops, prevents, or reduces the frequency, rate or extent of immature T cell proliferation in the thymus.
	GO:0009968	negative regulation of signal transduction	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction.
	GO:0033089	positive regulation of T cell differentiation in thymus	Any process that activates or increases the frequency, rate or extent of T cell differentiation in the thymus.
	GO:0046638	positive regulation of alpha-beta T cell differentiation	Any process that activates or increases the frequency, rate or extent of alpha-beta T cell differentiation.
	GO:0032332	positive regulation of chondrocyte differentiation	Any process that activates or increases the frequency, rate or extent of chondrocyte differentiation.
	GO:0050679	positive regulation of epithelial cell proliferation	Any process that activates or increases the rate or extent of epithelial cell proliferation.
	GO:0045880	positive regulation of smoothened signaling pathway	Any process that activates or increases the frequency, rate or extent of smoothened signaling.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0045595	regulation of cell differentiation	Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
	GO:0032355	response to estradiol	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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
	GO:0001501	skeletal system development	The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
	GO:0007224	smoothened signaling pathway	A series of molecular signals generated as a consequence of activation of the transmembrane protein Smoothened.
	GO:0061053	somite development	The progression of a somite from its initial formation to the mature structure. Somites are mesodermal clusters that are arranged segmentally along the anterior posterior axis of an embryo.
cellular component
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ser B:53 - Pro B:54	[ RasMol ]

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UniProtKB/Swiss-Prot
	IHH_HUMAN \| Q14623	:	3k7g 3k7h 3k7i 3n1f 3n1m 3n1o 3n1p

3k7g	THE INDIAN HEDGEHOG N-TERMINAL SIGNALLING DOMAIN, WILD TYPE
3k7h	THE E95K MUTANT OF THE INDIAN HEDGEHOG N-TERMINAL SIGNALLING DOMAIN
3k7i	THE E131K MUTANT OF THE INDIAN HEDGEHOG N-TERMINAL SIGNALLING DOMAIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (5, 5)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 1)

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Pfam Domains (1, 1)

Gene Ontology (33, 33)

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