3Q91 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HUMAN URIDINE DIPHOSPHATE GLUCOSE PYROPHOSPHATASE (NUDT14)

Authors :   L. Tresaugues, M. I. Siponen, C. H. Arrowsmith, H. Berglund, C. Bountra R. Collins, A. M. Edwards, T. Ekblad, S. Flodin, A. Flores, S. Graslund M. Hammarstrom, I. Johansson, T. Karlberg, S. Kol, T. Kotenyova, E. Kouznetsova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, A. G. Thorsell, S. Van Der Berg, E. Wahlberg, J. Weigelt, M. Welin, P. Structural Genomics Consortium (Sgc)

Date :   07 Jan 11 (Deposition) - 16 Feb 11 (Release) - 16 Feb 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Structural Genomics, Structural Genomics Consortium, Sgc, Nudix, Mutt-Like, Hydrolase, Magnesium Binding (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, T. Ekblad, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Johansson, T. Karlberg, S. Kol, T. Kotenyova, E. Kouznetsova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, A. G. Thorsell, S. Van Der Berg, E. Wahlberg, J. Weigelt, M. Welin, P. Nordlund
Crystal Structure Of Human Uridine Diphosphate Glucose Pyrophosphatase (Nudt14)
To Be Published
PubMed: search

Molecule 1 - URIDINE DIPHOSPHATE GLUCOSE PYROPHOSPHATASE
	Chains	:	A, C, B, D
	EC Number	:	3.6.1.45
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21 (DE3) R3 PRARE
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 28-222
	Gene	:	NUDT14, UGPP
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	UDPG PYROPHOSPHATASE, UGPPASE, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 14, NUDIX MOTIF 14

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3Q91)

(no "Site" information available for 3Q91)

(no "SS Bond" information available for 3Q91)

(no "Cis Peptide Bond" information available for 3Q91)

(no "SAP(SNP)/Variant" information available for 3Q91)

(no "PROSITE Motif" information available for 3Q91)

(no "Exon" information available for 3Q91)

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:145
 aligned with NUD14_HUMAN | O95848 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:182
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218  
          NUD14_HUMAN    39 THDSVTVLLFNSSRRSLVLVKQFRPAVYAGEVERRFPGSLAAVDQDGPRELQPALPGSAGVTVELCAGLVDQPGLSLEEVACKEAWEECGYHLAPSDLRRVATYWSGVGLTGSRQTMFYTEVTDAQRSGPGGGLVEEGELIEVVHLPLEGAQAFADDPDIPKTLGVIFGVSWFLSQVAPNLD 220
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eeeeeeeehhhhhhhhh.-------------------------..eeee.eeee......hhhhhhhhhhhhhhh...hhhhheeeeeeee.---..eeeeeeeeeehhhhh.---------...eeeeeee..hhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q91 A  39 THDSVTVLLFNSSRRSLVLVKQFRPAVYAGEVE-------------------------AGVTVELCAGLVDQPGLSLEEVACKEAWEECGYHLAPSDLRRVATYWSG---TGSRQTMFYTEVTDAQRS---------GELIEVVHLPLEGAQAFADDPDIPKTLGVIFGVSWFLSQVAPNLD 220
                                    48        58        68  |      -         -        98       108       118       128       138      |  -|      158       | -       178       188       198       208       218  
                                                           71                        97                                             145 149              166       176

Chain B from PDB  Type:PROTEIN  Length:131
 aligned with NUD14_HUMAN | O95848 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:181
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 
          NUD14_HUMAN    40 HDSVTVLLFNSSRRSLVLVKQFRPAVYAGEVERRFPGSLAAVDQDGPRELQPALPGSAGVTVELCAGLVDQPGLSLEEVACKEAWEECGYHLAPSDLRRVATYWSGVGLTGSRQTMFYTEVTDAQRSGPGGGLVEEGELIEVVHLPLEGAQAFADDPDIPKTLGVIFGVSWFLSQVAPNLD 220
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....eeeeeee------------------------------------...eee.eeee......hhhhhhhhhhhhhhh...hhhhheeeeeee...----.eeeeeeeeehhhhh..----------..eeeeee..hhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q91 B  40 HDSVTVLLFNSSRRSLVLVKQ------------------------------------AGVTVELCAGLVDQPGLSLEEVACKEAWEECGYHLAPSDLRRVATYWSGV----SRQTMFYTEVTDAQRSG----------LIEVVHLPLEGAQAFADDPDIPKTLGVIFGVSWFLSQVAPNLD 220
                                    49        59|        -         -         -       |99       109       119       129       139      |  - |     159       | -       179       189       199       209       219 
                                               60                                   97                                              146  151             167        178

Chain C from PDB  Type:PROTEIN  Length:146
 aligned with NUD14_HUMAN | O95848 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:181
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219 
          NUD14_HUMAN    40 HDSVTVLLFNSSRRSLVLVKQFRPAVYAGEVERRFPGSLAAVDQDGPRELQPALPGSAGVTVELCAGLVDQPGLSLEEVACKEAWEECGYHLAPSDLRRVATYWSGVGLTGSRQTMFYTEVTDAQRSGPGGGLVEEGELIEVVHLPLEGAQAFADDPDIPKTLGVIFGVSWFLSQVAPNLD 220
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee....eeeeeeeehhhhhhhhhhh------------------------..eeee.eeee......hhhhhhhhhhhhh.....hhhhheeeeeeee..--..eeeeeeeeeehhhhh.---------...eeeeeee..hhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q91 C  40 HDSVTVLLFNSSRRSLVLVKQFRPAVYAGEVER------------------------AGVTVELCAGLVDQPGLSLEEVACKEAWEECGYHLAPSDLRRVATYWSGV--TGSRQTMFYTEVTDAQRS---------GELIEVVHLPLEGAQAFADDPDIPKTLGVIFGVSWFLSQVAPNLD 220
                                    49        59        69  |      -         -       |99       109       119       129       139      |149       159      |  -      |179       189       199       209       219 
                                                           72                       97                                              146  |              166       176                                            
                                                                                                                                       149

Chain D from PDB  Type:PROTEIN  Length:149
 aligned with NUD14_HUMAN | O95848 from UniProtKB/Swiss-Prot  Length:222

    Alignment length:182
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218  
          NUD14_HUMAN    39 THDSVTVLLFNSSRRSLVLVKQFRPAVYAGEVERRFPGSLAAVDQDGPRELQPALPGSAGVTVELCAGLVDQPGLSLEEVACKEAWEECGYHLAPSDLRRVATYWSGVGLTGSRQTMFYTEVTDAQRSGPGGGLVEEGELIEVVHLPLEGAQAFADDPDIPKTLGVIFGVSWFLSQVAPNLD 220
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) NUDIX-3q91D01 D:39-205                                                                                                                                                 --------------- Pfam domains (1)
           Pfam domains (2) NUDIX-3q91D02 D:39-205                                                                                                                                                 --------------- Pfam domains (2)
           Pfam domains (3) NUDIX-3q91D03 D:39-205                                                                                                                                                 --------------- Pfam domains (3)
           Pfam domains (4) NUDIX-3q91D04 D:39-205                                                                                                                                                 --------------- Pfam domains (4)
         Sec.struct. author ...eeeeeeee....eeeeeeeehhhhhhhhhh..-------------------......eeee.eeee......hhhhhhhhhhhhhhh........eeeeeeee..--..eeeeeeeeeehhhhh------------..eeeeee..hhhhhhhh.....hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q91 D  39 THDSVTVLLFNSSRRSLVLVKQFRPAVYAGEVERR-------------------LPGSAGVTVELCAGLVDQPGLSLEEVACKEAWEECGYHLAPSDLRRVATYWSGV--TGSRQTMFYTEVTDAQR------------LIEVVHLPLEGAQAFADDPDIPKTLGVIFGVSWFLSQVAPNLD 220
                                    48        58        68    |    -         -    |   98       108       118       128       138       | -|      158      |  -       178       188       198       208       218  
                                                             73                  93                                                  146  |             165          178                                          
                                                                                                                                        149

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 '\|'

(no "SCOP Domain" information available for 3Q91)

(no "CATH Domain" information available for 3Q91)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NUDIX (85)

Family: NUDIX (78)

Homo sapiens (Human) (12)

1a	NUDIX-3q91D01	D:39-205
1b	NUDIX-3q91D02	D:39-205
1c	NUDIX-3q91D03	D:39-205
1d	NUDIX-3q91D04	D:39-205

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (NUD14_HUMAN | O95848)

molecular function
	GO:0047631	ADP-ribose diphosphatase activity	Catalysis of the reaction: ADP-ribose + H2O = AMP + D-ribose 5-phosphate.
	GO:0008768	UDP-sugar diphosphatase activity	Catalysis of the reaction: UDP-sugar + H2O = UMP + sugar 1-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:0016818	hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	Catalysis of the hydrolysis of any acid anhydride which contains phosphorus.
	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:0018279	protein N-linked glycosylation via asparagine	The glycosylation of protein via the N4 atom of peptidyl-asparagine forming N4-glycosyl-L-asparagine; the most common form is N-acetylglucosaminyl asparagine; N-acetylgalactosaminyl asparagine and N4 glucosyl asparagine also occur. This modification typically occurs in extracellular peptides with an N-X-(ST) motif. Partial modification has been observed to occur with cysteine, rather than serine or threonine, in the third position; secondary structure features are important, and proline in the second or fourth positions inhibits modification.
cellular component
	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.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3q91)

Biological Units
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	3q91
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Ligands, Modified Residues, Ions (0, 0)

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