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(-) Description

Title :  CRYSTAL STRUCTURE OF THE N-TERMINAL SIGNALLING DOMAIN OF HUMAN DHH WITHOUT CALCIUM
 
Authors :  B. Bishop, A. R. Aricescu, K. Harlos, C. A. O'Callaghan, E. Y. Jones, C.
Date :  14 Apr 09  (Deposition) - 30 Jun 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipoprotein, Development, Cell Membrane, Autocatalytic Cleavage, Signaling Protein, Disease Mutation, Hedgehog Signalling, Protease, Membrane, Secreted, Palmitate, Hydrolase, Signal Transduction, Developmental Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Bishop, A. R. Aricescu, K. Harlos, C. A. O'Callaghan, E. Y. Jones, C. Siebold
Structural Insights Into Hedgehog Ligand Sequestration By The Human Hedgehog-Interacting Protein Hip
Nat. Struct. Mol. Biol. V. 16 698 2009
PubMed-ID: 19561611  |  Reference-DOI: 10.1038/NSMB.1607

(-) Compounds

Molecule 1 - DESERT HEDGEHOG PROTEIN N-PRODUCT
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System Taxid562
    FragmentN-TERMINAL SIGNALLING DOMAIN, RESIDUES 39-194
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDESERT HEDGEHOG, HHG-3, DHH

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:141 , ASP A:148 , HIS A:183 , HIS A:203BINDING SITE FOR RESIDUE ZN A1204
2AC2SOFTWARELYS A:88 , ARG A:124 , THR A:126 , ARG A:154BINDING SITE FOR RESIDUE SO4 A1205

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WFQ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Val A:49 -Pro A:50

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054873L162PDHH_HUMANDisease (SRXY7)111033589AL162P

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WFQ)

(-) Sequences/Alignments

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:164
 aligned with DHH_HUMAN | O43323 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:315
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349     
            DHH_HUMAN    40 LVPLLYKQFVPGVPERTLGASGPAEGRVARGSERFRDLVPNYNPDIIFKDEENSGADRLMTERCKERVNALAIAVMNMWPGVRLRVTEGWDEDGHHAQDSLHYEGRALDITTSDRDRNKYGLLARLAVEAGFDWVYYESRNHVHVSVKADNSLAVRAGGCFPGNATVRLWSGERKGLRELHRGDWVLAADASGRVVPTPVLLFLDRDLQRRASFVAVETEWPPRKLLLTPWHLVFAARGPAPAPGDFAPVFARRLRAGDSVLAPGGDALRPARVARVAREEAVGVFAPLTAHGTLLVNDVLASCYAVLESHQWAH 354
               SCOP domains d2wfqa_ A: automated matches                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2wfqA00 A:40-203  [code=3.30.1380.10, no name defined]                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains HH_signal-2wfqA02 A:40-185                                                                                                                        --Hint-2w---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........ee......................hhhhhhee.....eee......hhh.eehhhhhhhhhhhhhhhhhhh....eeeee...........hhhhhh.eeeeee...hhhhhhhhhhhhhhh...eeeeee..eeeee.....hhhhh-------------------------------------------------------------------------------------------------------------------------------------------------------hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------P------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfq A  40 LVPLLYKQFVPGVPERTLGASGPAEGRVARGSERFRDLVPNYNPDIIFKDEENSGADRLMTERCKERVNALAIAVMNMWPGVRLRVTEGWDEDGHHAQDSLHYEGRALDITTSDRDRNKYGLLARLAVEAGFDWVYYESRNHVHVSVKADNSLAVK-------------------------------------------------------------------------------------------------------------------------------------------------------LEHHHHHH 203
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189     |   -         -         -         -         -         -         -         -         -         -         -         -         -         -         -       198     
                                                                                                                                                                                     195                                                                                                                                                     196       

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: H-int (15)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DHH_HUMAN | O43323)
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.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0033327    Leydig cell differentiation    The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a Leydig cell. A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
    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:0030238    male sex determination    The specification of male sex of an individual organism.
    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:0042552    myelination    The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0050810    regulation of steroid biosynthetic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    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:0043627    response to estrogen    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 an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
    GO:0007286    spermatid development    The process whose specific outcome is the progression of a spermatid over time, from its formation to the mature structure.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DHH_HUMAN | O433232wfr 2wg3 3n1g 3n1q

(-) Related Entries Specified in the PDB File

2wfr CRYSTAL STRUCTURE OF THE N-TERMINAL SIGNALLING DOMAIN OF HUMAN DHH WITH CALCIUM
2wft CRYSTAL STRUCTURE OF THE HUMAN HIP ECTODOMAIN
2wfx CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN HEDGEHOG-INTERACTING PROTEIN HIP AND SONIC HEDGEHOG IN THE PRESENCE OF CALCIUM
2wg3 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN HEDGEHOG-INTERACTING PROTEIN HIP AND DESERT HEDGEHOG WITHOUT CALCIUM
2wg4 CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN HUMAN HEDGEHOG-INTERACTING PROTEIN HIP AND SONIC HEDGEHOG WITHOUT CALCIUM