2VR2 - JenaLib

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Title :   HUMAN DIHYDROPYRIMIDINASE

Authors :   M. Welin, T. Karlberg, J. Andersson, C. H. Arrowsmith, H. Berglund, R. D R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Gras M. Hammarstrom, M. D. Herman, I. Johansson, A. Kallas, T. Kotenyova, L M. Moche, M. E. Nilsson, T. Nyman, C. Persson, J. Sagemark, L. Svensson A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Wikstr P. Nordlund, Structural Genomics Consortium (Sgc)

Date :   25 Mar 08 (Deposition) - 01 Apr 08 (Release) - 06 May 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Hydantoinase, Metal-Binding, Disease Mutation, Dihydropyrimidine Amidohydrolase, Dihydropyrimidinase, Nucleotide Metabolism, Dhp, Dpys, Dhpase, Hydrolase, Zn-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Welin, T. Karlberg, J. Andersson, C. H. Arrowsmith, H. Berglund, R. D. Busam, R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, M. D. Herman, I. Johansson, A. Kallas, T. Kotenyova, L. Lehtio, M. Moche, M. E. Nilsson, T. Nyman, C. Persson, J. Sagemark, L. Svensson, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Wikstrom, P. Nordlund
The Crystal Structure Of Human Dihydropyrimidinase
To Be Published
PubMed: search

Molecule 1 - DIHYDROPYRIMIDINASE
	Chains	:	A
	EC Number	:	3.5.2.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21DE3
	Expression System Taxid	:	469008
	Expression System Vector	:	PNIC-BSA4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DHPASE, DHP, DIHYDROPYRIMIDINE AMIDOHYDROLASE, HYDANTOINASE

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:67 , HIS A:69 , LYS A:159 , ASP A:326 , ZN A:1495 , HOH A:2001	BINDING SITE FOR RESIDUE ZN A1494
2	AC2	SOFTWARE	LYS A:159 , HIS A:192 , HIS A:248 , ZN A:1494	BINDING SITE FOR RESIDUE ZN A1495
3	AC3	SOFTWARE	LYS A:88	BINDING SITE FOR RESIDUE CL A1496

(no "SS Bond" information available for 2VR2)

Asymmetric Unit

No.	Residues
1	Gly A:298	-	Pro A:299
2	Tyr A:389	-	Pro A:390

Asymmetric Unit (5, 5)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_002267	T	68	R	DPYS_HUMAN	Disease (DPYSD)	---	A	T	68	R
2	UniProt	VAR_002268	Q	334	R	DPYS_HUMAN	Disease (DPYSD)	121964923	A	Q	334	R
3	UniProt	VAR_002269	W	360	R	DPYS_HUMAN	Disease (DPYSD)	121964924	A	W	360	R
4	UniProt	VAR_002270	G	435	R	DPYS_HUMAN	Disease (DPYSD)	267606773	A	G	435	R
5	UniProt	VAR_002271	R	490	T	DPYS_HUMAN	Disease (DPYSD)	---	A	R	490	T

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

Biological Unit 1 (5, 20)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_002267	T	68	R	DPYS_HUMAN	Disease (DPYSD)	---	A	T	68	R
2	UniProt	VAR_002268	Q	334	R	DPYS_HUMAN	Disease (DPYSD)	121964923	A	Q	334	R
3	UniProt	VAR_002269	W	360	R	DPYS_HUMAN	Disease (DPYSD)	121964924	A	W	360	R
4	UniProt	VAR_002270	G	435	R	DPYS_HUMAN	Disease (DPYSD)	267606773	A	G	435	R
5	UniProt	VAR_002271	R	490	T	DPYS_HUMAN	Disease (DPYSD)	---	A	R	490	T

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

(no "PROSITE Motif" information available for 2VR2)

(no "Exon" information available for 2VR2)

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:478
 aligned with DPYS_HUMAN | Q14117 from UniProtKB/Swiss-Prot  Length:519

    Alignment length:489
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484         
           DPYS_HUMAN     5 SRLLIRGGRVVNDDFSEVADVLVEDGVVRALGHDLLPPGGAPAGLRVLDAAGKLVLPGGIDTHTHMQFPFMGSRSIDDFHQGTKAALSGGTTMIIDFAIPQKGGSLIEAFETWRSWADPKVCCDYSLHVAVTWWSDQVKEEMKILVQDKGVNSFKMFMAYKDLYMVTDLELYEAFSRCKEIGAIAQVHAENGDLIAEGAKKMLALGITGPEGHELCRPEAVEAEATLRAITIASAVNCPLYIVHVMSKSAAKVIADARRDGKVVYGEPIAASLGTDGTHYWNKEWHHAAHHVMGPPLRPDPSTPDFLMNLLANDDLTTTGTDNCTFNTCQKALGKDDFTKIPNGVNGVEDRMSVIWEKGVHSGKMDENRFVAVTSTNAAKIFNLYPRKGRIAVGSDADIVIWDPKGTRTISAKTHHQAVNFNIFEGMVCHGVPLVTISRGKVVYEAGVFSVTAGDGKFIPRKPFAEYIYKRIKQRDRTCTPTPVERAPY 493
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------------------------Amidohydro_1-2vr2A01 A:58-407                                                                                                                                                                                                                                                                                                                                 -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee....eee.eeeee..eeeeee.-----------.eeee....eeee.eeeeee...............hhhhhhhhh..eeeeeeee......hhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhhhhh.eeeee..hhhhhhhhhhhhhhh....hhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhh...eeeeehhhhhhh.hhhhhh.hhhhhhh...........hhhhhhhhhhhh.............hhhhhhhhh.hhhhh........hhhhhhhhhhh.....hhhhhhhhhhhhhhhhh................eeeeeeeeeee..................eeeeeeeeeee..eeeee..ee...............hhhhhhhhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------R-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R-------------------------R--------------------------------------------------------------------------R------------------------------------------------------T--- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vr2 A   5 SRLLIRGGRVVNDDFSEVADVLVEDGVVRALGH-----------LRVLDAAGKLVLPGGIDTHTHMQFPFMGSRSIDDFHQGTKAALSGGTTMIIDFAIPQKGGSLIEAFETWRSWADPKVCCDYSLHVAVTWWSDQVKEEMKILVQDKGVNSFKMFMAYKDLYMVTDLELYEAFSRCKEIGAIAQVHAENGDLIAEGAKKMLALGITGPEGHELCRPEAVEAEATLRAITIASAVNCPLYIVHVMSKSAAKVIADARRDGKVVYGEPIAASLGTDGTHYWNKEWHHAAHHVMGPPLRPDPSTPDFLMNLLANDDLTTTGTDNCTFNTCQKALGKDDFTKIPNGVNGVEDRMSVIWEKGVHSGKMDENRFVAVTSTNAAKIFNLYPRKGRIAVGSDADIVIWDPKGTRTISAKTHHQAVNFNIFEGMVCHGVPLVTISRGKVVYEAGVFSVTAGDGKFIPRKPFAEYIYKRIKQRDRTCTPTPVERAPY 493
                                    14        24        34  |      -    |   54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484         
                                                           37          49

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 2VR2)

(no "CATH Domain" information available for 2VR2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: Amidohydro_1 (28)

Homo sapiens (Human) (3)

Amidohydro_1-2vr2A01

A:58-407

Asymmetric Unit(hide GO term definitions)

Chain A (DPYS_HUMAN | Q14117)

molecular function
	GO:0016597	amino acid binding	Interacting selectively and non-covalently with an amino acid, organic acids containing one or more amino substituents.
	GO:0004157	dihydropyrimidinase activity	Catalysis of the reaction: 5,6-dihydrouracil + H2O = 3-ureidopropionate.
	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:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0051219	phosphoprotein binding	Interacting selectively and non-covalently with a phosphorylated protein.
	GO:0002059	thymine binding	Interacting selectively and non-covalently with thymine.
	GO:0002058	uracil binding	Interacting selectively and non-covalently with uracil.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0019482	beta-alanine metabolic process	The chemical reactions and pathways involving beta-alanine (3-aminopropanoic acid), an achiral amino acid and an isomer of alanine. It occurs free (e.g. in brain) and in combination (e.g. in pantothenate) but it is not a constituent of proteins.
	GO:0051260	protein homooligomerization	The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0006208	pyrimidine nucleobase catabolic process	The chemical reactions and pathways resulting in the breakdown of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
	GO:0046135	pyrimidine nucleoside catabolic process	The chemical reactions and pathways resulting in the breakdown of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
	GO:0006210	thymine catabolic process	The chemical reactions and pathways resulting in the breakdown of thymine, 5-methyluracil, one of the two major pyrimidine bases present (as thymidine) in DNA but not found in RNA other than (as ribothymidine) in transfer RNA, where it is a minor base.
	GO:0006212	uracil catabolic process	The chemical reactions and pathways resulting in the breakdown of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA.
	GO:0019860	uracil metabolic process	The chemical reactions and pathways involving uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA.
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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		Tyr A:389 - Pro A:390	[ RasMol ]

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Description

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