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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT INTO ITS ROLE AS A TUMOR SUPPRESSOR
 
Authors :  J. Hwang, Y. Kim, H. Lee, M. H. Kim
Date :  29 Jul 10  (Deposition) - 19 Jan 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Hwang, Y. Kim, H. B. Kang, L. Jaroszewski, A. Deacon, H. Lee, W. C. Choi, K. J. Kim, C. H. Kim, B. S. Kang, J. O. Lee, T. K. Oh, J. W. Kim, I. A. Wilson, M. H. Kim
Crystal Structure Of Human Ndrg2 Protein Provides Insight Into Its Role As A Tumor Suppressor.
J. Biol. Chem. V. 286 12450 2011
PubMed-ID: 21247902  |  Reference-DOI: 10.1074/JBC.M110.170803

(-) Compounds

Molecule 1 - PROTEIN NDRG2
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentALPHA-BETA HYDROLASE DOMAIN, RESIDUES 24-304
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNDRG2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:41 , TYR B:61 , PHE B:69 , GLN B:75 , ARG B:83 , HIS B:85 , HOH B:2023BINDING SITE FOR RESIDUE ACT B1305
2AC2SOFTWARETYR A:41 , TYR A:61 , PHE A:69 , GLN A:75 , ARG A:83 , HIS A:85BINDING SITE FOR RESIDUE ACT A1305
3AC3SOFTWARETYR C:41 , TYR C:61 , PHE C:69 , GLN C:75 , ARG C:83 , HIS C:85BINDING SITE FOR RESIDUE ACT C1305

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 6)

Asymmetric Unit (2, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050236T45SNDRG2_HUMANPolymorphism36007455A/B/CT31S
2UniProtVAR_026572G48VNDRG2_HUMANPolymorphism11552412A/B/CG34V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050236T45SNDRG2_HUMANPolymorphism36007455AT31S
2UniProtVAR_026572G48VNDRG2_HUMANPolymorphism11552412AG34V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050236T45SNDRG2_HUMANPolymorphism36007455BT31S
2UniProtVAR_026572G48VNDRG2_HUMANPolymorphism11552412BG34V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050236T45SNDRG2_HUMANPolymorphism36007455CT31S
2UniProtVAR_026572G48VNDRG2_HUMANPolymorphism11552412CG34V

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XMQ)

(-) 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:281
 aligned with NDRG2_HUMAN | Q9UN36 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:281
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317 
          NDRG2_HUMAN    38 GQTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQEIIQNFVRVHVDAPGMEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMDWAAHKLTGLTSSIPEMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIELYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDAVVECNSKLDPTQTSFLKMADSGGQPQLTQPGKLTEAFKYFLQGMGYMA 318
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeeee........eeeee.....hhhhhhhhhhhhhhhhhhhh...eeeee..................hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.................eeeeee....hhhhhhhhhhhh....eeeeee.....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------S--V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xmq A  24 AKTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQEIIQNFVRVHVDAPGMEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMDWAAHKLTGLTSSIPEMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIENYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDAVVECNSKLDPTQTSFLKMADSGGQPQLTQPGKLTEAFKYFLQGMGYMA 304
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303 

Chain B from PDB  Type:PROTEIN  Length:281
 aligned with NDRG2_HUMAN | Q9UN36 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:281
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317 
          NDRG2_HUMAN    38 GQTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQEIIQNFVRVHVDAPGMEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMDWAAHKLTGLTSSIPEMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIELYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDAVVECNSKLDPTQTSFLKMADSGGQPQLTQPGKLTEAFKYFLQGMGYMA 318
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeeee........eeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeee..................hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh.................eeeeee....hhhhhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------S--V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xmq B  24 AKTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQEIIQNFVRVHVDAPGMEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMDWAAHKLTGLTSSIPEMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIENYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDAVVECNSKLDPTQTSFLKMADSGGQPQLTQPGKLTEAFKYFLQGMGYMA 304
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303 

Chain C from PDB  Type:PROTEIN  Length:281
 aligned with NDRG2_HUMAN | Q9UN36 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:281
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317 
          NDRG2_HUMAN    38 GQTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQEIIQNFVRVHVDAPGMEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMDWAAHKLTGLTSSIPEMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIELYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDAVVECNSKLDPTQTSFLKMADSGGQPQLTQPGKLTEAFKYFLQGMGYMA 318
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeeee........eeeee.....hhhhhhhhhhhhhhhhhhhh...eeeee..................hhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh................eeeeee....hhhhhhhhhh..hhh.eeeeee.....hhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------S--V------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xmq C  24 AKTHSVETPYGSVTFTVYGTPKPKRPAILTYHDVGLNYKSCFQPLFQFEDMQEIIQNFVRVHVDAPGMEEGAPVFPLGYQYPSLDQLADMIPCVLQYLNFSTIIGVGVGAGAYILARYALNHPDTVEGLVLINIDPNAKGWMDWAAHKLTGLTSSIPEMILGHLFSQEELSGNSELIQKYRNIITHAPNLDNIENYWNSYNNRRDLNFERGGDITLRCPVMLVVGDQAPHEDAVVECNSKLDPTQTSFLKMADSGGQPQLTQPGKLTEAFKYFLQGMGYMA 304
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303 

   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  (0, 0)

(no "SCOP Domain" information available for 2XMQ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XMQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XMQ)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (NDRG2_HUMAN | Q9UN36)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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).
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    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: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:0070373    negative regulation of ERK1 and ERK2 cascade    Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0001818    negative regulation of cytokine production    Any process that stops, prevents, or reduces the rate of production of a cytokine.
    GO:0048662    negative regulation of smooth muscle cell proliferation    Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0090361    regulation of platelet-derived growth factor production    Any process that modulates the rate, frequency, or extent of the appearance of any platelet-derived growth factor due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0010574    regulation of vascular endothelial growth factor production    Any process that modulates the frequency, rate, or extent of production of vascular endothelial growth factor.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0021762    substantia nigra development    The progression of the substantia nigra over time from its initial formation until its mature state. The substantia nigra is the layer of gray substance that separates the posterior parts of the cerebral peduncles (tegmentum mesencephali) from the anterior parts; it normally includes a posterior compact part with many pigmented cells (pars compacta) and an anterior reticular part whose cells contain little pigment (pars reticularis).
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NDRG2_HUMAN | Q9UN362xmr 2xms

(-) Related Entries Specified in the PDB File

2xmr CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT INTO ITS ROLE AS A TUMOR SUPPRESSOR
2xms CRYSTAL STRUCTURE OF HUMAN NDRG2 PROTEIN PROVIDES INSIGHT INTO ITS ROLE AS A TUMOR SUPPRESSOR