3GG6 - JenaLib

Title :   CRYSTAL STRUCTURE OF THE NUDIX DOMAIN OF HUMAN NUDT18

Authors :   L. Tresaugues, M. I. Siponen, L. Lehtio, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, T. Karlberg, T. Kotenyova, M. Moche, M. E. Nilsson, T. Nyman, C. Persson, J. Sagemark, H. Schueler, A. G. Thorsell, S. Van Den Berg J. Weigelt, M. Welin, M. Wisniewska, P. Nordlund, Structural Genomics Consortium (Sgc)

Date :   27 Feb 09 (Deposition) - 10 Mar 09 (Release) - 24 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A

Keywords :   Nudix, Nudt18, Nxr1, Nucleotide Hydrolase, Hydrolase, Structural Genomics, Structural Genomics Consortium, Sgc, Sgc Stockholm, Alternative Splicing, Magnesium, Manganese, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Tresaugues, M. I. Siponen, L. Lehtio, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, T. Karlberg, T. Kotenyova, M. Moche, M. E. Nilsson, T. Nyman, C. Persson, J. Sagemark, H. Schueler, A. G. Thorsell, S. Van Den Berg, J. Weigelt, M. Welin, M. Wisniewska, P. Nordlund
Crystal Structure Of The Nudix Domain Of Human Nudt18
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 18
	Chains	:	A
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	NUDIX HYDROLASE DOMAIN
	Gene	:	NUDT18
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NUDIX MOTIF 18

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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

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Chain A from PDB  Type:PROTEIN  Length:144
 aligned with NUD18_HUMAN | Q6ZVK8 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:144
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175    
          NUD18_HUMAN    36 VRLRKNVCYVVLAVFLSEQDEVLLIQEAKRECRGSWYLPAGRMEPGETIVEALQREVKEEAGLHCEPETLLSVEERGPSWVRFVFLARPTGGILKTSKEADAESLQAAWYPRTSLPTPLRAHDILHLVELAAQYRQQARHPLIL 179
               SCOP domains d3gg6a_ A: automated matches                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeeeee......eeeeee.........ee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeeee....eeeeeeeeeeeee...hhhhh.....eeeeee...........hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -NUDIX  PDB: A:37-167 UniProt: 37-167                                                                                               ------------ PROSITE (1)
                PROSITE (2) ----------------------------------------NUDIX_BOX  PDB: A:76-9---------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gg6 A  36 VRLRKNVCYVVLAVFLSEQDEVLLIQEAKRECRGSWYLPAGRMEPGETIVEALQREVKEEAGLHCEPETLLSVEERGPSWVRFVFLARPTGGILKTSKEADAESLQAAWYPRTSLPTPLRAHDILHLVELAAQYRQQARHPLIL 179
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175

Legend:		→ Mismatch	(orange background)
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	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NUD18_HUMAN | Q6ZVK8)

molecular function
	GO:0044717	8-hydroxy-dADP phosphatase activity	Catalysis of the reaction8-hydroxy-dADP + H2O = 8-hydroxy-dAMP + phosphate.
	GO:0044716	8-oxo-GDP phosphatase activity	Catalysis of the reaction 8-oxo-GDP + H2O = 8-oxo-GMP + phosphate.
	GO:0044715	8-oxo-dGDP phosphatase activity	Catalysis of the reaction 8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0046712	GDP catabolic process	The chemical reactions and pathways resulting in the breakdown of GDP, guanosine 5'-diphosphate.
	GO:0046057	dADP catabolic process	The chemical reactions and pathways resulting in the breakdown of dADP, deoxyadenosine diphosphate (2'-deoxyadenosine 5'-diphosphate).
	GO:0046067	dGDP catabolic process	The chemical reactions and pathways resulting in the breakdown of dGDP, deoxyguanosine diphosphate, (2'-deoxyguanosine 5'-diphosphate).
	GO:0034656	nucleobase-containing small molecule catabolic process	The chemical reactions and pathways resulting in the breakdown of a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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		Thr A:152 - Pro A:153	[ RasMol ]

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