2G09 - JenaLib

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Title :   X-RAY STRUCTURE OF MOUSE PYRIMIDINE 5'-NUCLEOTIDASE TYPE 1, PRODUCT COMPLEX

Authors :   E. Bitto, C. A. Bingman, G. E. Wesenberg, G. N. Phillips Jr. , Center Fo Eukaryotic Structural Genomics (Cesg)

Date :   11 Feb 06 (Deposition) - 04 Apr 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Uniprot Q9D020, Umph-1, Cytosolic 5'-Nucleotidase Iii, Pyrimidine 5'- Nucleotidase 1, P5N-1, Nt5C3 Protein, Aah38029, Bc038029, Mm. 158936, Lead Poisoning, Structural Genomics Functional Follow-Up Study, Protein Structure Initiative, Psi, Center For Eukaryotic Structural Genomics, Cesg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Bitto, C. A. Bingman, G. E. Wesenberg, J. G. Mccoy, G. N. Phillips
Structure Of Pyrimidine 5'-Nucleotidase Type 1. Insight Int Mechanism Of Action And Inhibition During Lead Poisoning.
J. Biol. Chem. V. 281 20521 2006
PubMed-ID: 16672222 | Reference-DOI: 10.1074/JBC.M602000200

Molecule 1 - CYTOSOLIC 5'-NUCLEOTIDASE III
	Chains	:	A, B
	EC Number	:	3.1.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PVP 16
	Expression System Strain	:	B834 P(RARE2)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NT5C3
	Organism Common	:	HOUSE MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090
	Synonym	:	CN-III, PYRIMIDINE 5'- NUCLEOTIDASE 1, P5'N-1, P5N-1, PN-I, LUPIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 22)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	MSE	16	Mod. Amino Acid	SELENOMETHIONINE
3	PIN	2	Ligand/Ion	PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
4	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 10)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	PIN	1	Ligand/Ion	PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 10)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	8	Mod. Amino Acid	SELENOMETHIONINE
3	PIN	1	Ligand/Ion	PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID)
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:49 , ASP A:51 , ASP A:238 , PO4 A:903 , HOH A:1119 , HOH A:1254	BINDING SITE FOR RESIDUE MG A 901
2	AC2	SOFTWARE	ASP B:49 , ASP B:51 , ASP B:238 , PO4 B:904 , HOH B:1265 , HOH B:1309	BINDING SITE FOR RESIDUE MG B 902
3	AC3	SOFTWARE	ASP A:49 , PHE A:50 , ASP A:51 , SER A:164 , ALA A:165 , GLY A:166 , LYS A:213 , MG A:901 , HOH A:930 , HOH A:1046	BINDING SITE FOR RESIDUE PO4 A 903
4	AC4	SOFTWARE	ASP B:49 , PHE B:50 , ASP B:51 , SER B:164 , ALA B:165 , GLY B:166 , LYS B:213 , MG B:902 , HOH B:948 , HOH B:1037	BINDING SITE FOR RESIDUE PO4 B 904
5	AC5	SOFTWARE	GLN A:294 , LYS A:295 , LEU A:297 , HOH A:1066 , HOH A:1135 , HOH A:1146	BINDING SITE FOR RESIDUE PIN A 905
6	AC6	SOFTWARE	GLN B:294 , LYS B:295 , LEU B:297 , HOH B:1216 , HOH B:1299	BINDING SITE FOR RESIDUE PIN B 906

(no "SS Bond" information available for 2G09)

(no "Cis Peptide Bond" information available for 2G09)

(no "SAP(SNP)/Variant" information available for 2G09)

(no "PROSITE Motif" information available for 2G09)

(no "Exon" information available for 2G09)

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:291
 aligned with 5NT3A_MOUSE | Q9D020 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:321
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 
          5NT3A_MOUSE    11 AVASASVCAVVAGVVLAQYIFTLKRKTGRKTKIIEMMPEFQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYNGKRCPTCHNIIDNCKLVTDECRRKLLQLKEQYYAIEVDPVLTVEEKFPYMVEWYTKSHGLLIEQGIPKAKLKEIVADSDVMLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIRQAGVYHSNVKVVSNFMDFDENGVLKGFKGELIHVFNKHDGALKNTDYFSQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVKEESLEVVNSILQKTL 331
               SCOP domains d2g                              09a_ A: Cytosolic 5'-nucleotidase III                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h------------------------------hhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhheeeee.........ee..ee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhh...eeee...hhhhhhhhhhhh......eeee...eee.....eeee........hhhhhhhhhhhhhhhh....eeeeee.hhhhhhh........eeeeeeee..hhhhhhhhhhhhh.eeee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g09 A   7 AVH------------------------------LKmmPEFQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFDmTLSRFSYNGKRCPTCHNIIDNCKLVTDECRRKLLQLKEQYYAIEVDPVLTVEEKFPYmVEWYTKSHGLLIEQGIPKAKLKEIVADSDVmLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIRQAGVYHSNVKVVSNFmDFDENGVLKGFKGELIHVFNKHDGALKNTDYFSQLKDNSNIILLGDSQGDLRmADGVANVEHILKIGYLNDRVDELLEKYmDSYDIVLVKEESLEVVNSILQKTL 297
                              |      -         -         -   | || 16        26        36        46     |  56        66        76        86        96       106   |   116       126       136    |  146       156       166       176       186     | 196       206       216       226       236       246       256       266      |276       286       296 
                              9                             10 ||                                     52-MSE                                                   110-MSE                        141-MSE                                            192-MSE                                              245-MSE                     273-MSE                    
                                                              12-MSE                                                                                                                                                                                                                                                                                         
                                                               13-MSE

Chain B from PDB  Type:PROTEIN  Length:291
 aligned with 5NT3A_MOUSE | Q9D020 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:321
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330 
          5NT3A_MOUSE    11 AVASASVCAVVAGVVLAQYIFTLKRKTGRKTKIIEMMPEFQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFDMTLSRFSYNGKRCPTCHNIIDNCKLVTDECRRKLLQLKEQYYAIEVDPVLTVEEKFPYMVEWYTKSHGLLIEQGIPKAKLKEIVADSDVMLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIRQAGVYHSNVKVVSNFMDFDENGVLKGFKGELIHVFNKHDGALKNTDYFSQLKDNSNIILLGDSQGDLRMADGVANVEHILKIGYLNDRVDELLEKYMDSYDIVLVKEESLEVVNSILQKTL 331
               SCOP domains d2g                              09b_ B: Cytosolic 5'-nucleotidase III                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..h------------------------------hhhhhhhhh..ee..hhhhhhhhhhhhhhhhhhheeeee.........ee..ee..hhhhhhhh....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh......hhhhhhhhhhhh...eeeeeeeehhhhhhhhhhh......eeeeee.eee.....eeee........hhhhhhhhhhhhhhhh....eeeeee.hhhhhhh........eeeeeeee..hhhhhhhhhhhhh.eeee....hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g09 B   7 AVH------------------------------LKmmPEFQKSSVRIKNPTRVEEIICGLIKGGAAKLQIITDFDmTLSRFSYNGKRCPTCHNIIDNCKLVTDECRRKLLQLKEQYYAIEVDPVLTVEEKFPYmVEWYTKSHGLLIEQGIPKAKLKEIVADSDVmLKEGYENFFGKLQQHGIPVFIFSAGIGDVLEEVIRQAGVYHSNVKVVSNFmDFDENGVLKGFKGELIHVFNKHDGALKNTDYFSQLKDNSNIILLGDSQGDLRmADGVANVEHILKIGYLNDRVDELLEKYmDSYDIVLVKEESLEVVNSILQKTL 297
                              |      -         -         -   | || 16        26        36        46     |  56        66        76        86        96       106   |   116       126       136    |  146       156       166       176       186     | 196       206       216       226       236       246       256       266      |276       286       296 
                              9                             10 ||                                     52-MSE                                                   110-MSE                        141-MSE                                            192-MSE                                              245-MSE                     273-MSE                    
                                                              12-MSE                                                                                                                                                                                                                                                                                         
                                                               13-MSE

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: Pyrimidine 5'-nucleotidase (UMPH-1) (13)

Protein domain: Cytosolic 5'-nucleotidase III (9)

Mouse (Mus musculus) [TaxId: 10090] (8)

1a	d2g09a_	A:
1b	d2g09b_	B:

(no "CATH Domain" information available for 2G09)

(no "Pfam Domain" information available for 2G09)

Asymmetric Unit(hide GO term definitions)

Chain A,B (5NT3A_MOUSE | Q9D020)

molecular function
	GO:0008253	5'-nucleotidase activity	Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + 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:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016791	phosphatase activity	Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0046085	adenosine metabolic process	The chemical reactions and pathways involving adenosine, adenine riboside, a ribonucleoside found widely distributed in cells of every type as the free nucleoside and in combination in nucleic acids and various nucleoside coenzymes.
	GO:0016311	dephosphorylation	The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2g09)

Biological Units
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	2g09
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	3.1.1.5
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	5NT3A_MOUSE \| Q9D020
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UniProtKB/Swiss-Prot
	5NT3A_MOUSE \| Q9D020	:	2bdu 2g06 2g07 2g08 2g0a 2q4t 4fe3 4kx3 4kx5

2bdu	MOUSE P5N-1 APO FORM
2g06	MOUSE P5N-1 WITH BOUND MAGNESIUM(II)
2g07	MOUSE P5N-1 PHOSPHO-ENZYME INTERMEDIATE ANALOG WITH BERYLLIUM FLUORIDE
2g08	MOUSE P5N-1 PRODUCT-TRANSITION COMPLEX ANALOG WITH ALUMINUM FLUORIDE
2g0a	MOUSE P5N-1 LEAD(II) BOUND IN ACTIVE SITE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 22)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

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