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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROTEIN SYNDESMOS (NUDT16-LIKE PROTEIN)
 
Authors :  L. Tresaugues, M. I. Siponen, C. H. Arrowsmith, H. Berglund, C. Bountra R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammar A. Johansson, I. Johansson, A. Kallas, T. Karlberg, T. Kotenyova, A. K P. Kraulis, M. Moche, T. K. Nielsen, T. Nyman, C. Persson, A. K. Roos, H. P. Schutz, A. G. Thorsell, S. Van Den Berg, J. Weigelt, M. Welin, M. Wi P. Nordlund, Structural Genomics Consortium (Sgc)
Date :  30 Nov 09  (Deposition) - 19 Jan 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Nudt16-Like, Nudt16L1, Syndesmos, Nudix, Rna Regulation, Rna-Binding, Structural Genomics Consortium, Sgc, Rna Degradation, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Tresaugues, M. I. Siponen, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, A. Kallas, T. Karlberg, T. Kotenyova, A. Kotzsch, P. Kraulis, M. Moche, T. K. Nielsen, T. Nyman, C. Persson, A. K. Roos, H. Schuler, P. Schutz, A. G. Thorsell, S. Van Den Berg, J. Weigelt, M. Welin, M. Wisniewska, P. Nordlund
Crystal Structure Of Human Protein Syndesmos (Nudt16L1)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROTEIN SYNDESMOS
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CH2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NUDT16L1, SDOS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUDT16-LIKE PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:188 , VAL A:189 , LEU A:192 , HOH A:327BINDING SITE FOR RESIDUE GOL A 1
2AC2SOFTWAREARG A:43 , GLN A:150 , LYS A:151BINDING SITE FOR RESIDUE CL A 219

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KVH)

(-) 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:192
 aligned with TIRR_HUMAN | Q9BRJ7 from UniProtKB/Swiss-Prot  Length:211

    Alignment length:199
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198         
           TIRR_HUMAN     9 LKQISRVEAMRLGPGWSHSCHAMLYAANPGQLFGRIPMRFSVLMQMRFDGLLGFPGGFVDRRFWSLEDGLNRVLGLGLGCLRLTEADYLSSHLTEGPHRVVAHLYARQLTLEQLHAVEISAVHSRDHGLEVLGLVRVPLYTQKDRVGGFPNFLSNAFVSTAKCQLLFALKVLNMMPEEKLVEALAAATEKQKKALEKLL 207
               SCOP domains d3kvha_ A: automated matches                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhhh......eeeeeeeeeeeeeeeehhheeeeeeeeeeee....ee..eeee.....hhhhhhhhh.....---..hhh.eeeeee.----.eeeeeeeee.hhhhhhhhhhhhhh.......eeeeeee..........hhhhhhh.....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kvh A   9 LKQISRVEAMRLGPGWSHSCHAMLYAANPGQLFGRIPMRFSVLMQMRFDGLLGFPGGFVDRRFWSLEDGLNRVLGLGL---RLTEADYLSSHLT----RVVAHLYARQLTLEQLHAVEISAVHSRDHGLEVLGLVRVPLYTQKDRVGGFPNFLSNAFVSTAKCQLLFALKVLNMMPEEKLVEALAAATEKQKKALEKLL 207
                                    18        28        38        48        58        68        78       | - |      98   |   108       118       128       138       148       158       168       178       188       198         
                                                                                                        86  90         102  107
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3KVH)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (TIRR_HUMAN | Q9BRJ7)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0050072    m7G(5')pppN diphosphatase activity    Catalysis of the reaction: 7-methylguanosine 5'-triphospho-5'-polynucleotide + H2O = 7-methylguanosine 5'-phosphate + polynucleotide.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0030515    snoRNA binding    Interacting selectively and non-covalently with small nucleolar RNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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