PDBsum entry 2j2c

Hydrolase

PDB id: 2j2c

Contents

Protein chain

470 a.a. *

Ligands

GOL

SO4 ×6

Metals

_MG

Waters ×445

* Residue conservation analysis

PDB id:

2j2c

Name:

Hydrolase

Title:

Crystal structure of human cytosolic 5'-nucleotidase ii (nt5c2, cn-ii)

Structure:

Cytosolic purine 5'-nucleotidase. Chain: a. Fragment: residues 1-536. Synonym: 5'-nucleotidase cytosolic ii, cytosolic purine 5'- nucleotidase. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: rosetta2(de).

Biol. unit:

Monomer (from PDB file)

Resolution:

2.20Å R-factor: 0.154 R-free: 0.184

Authors:

K.Wallden,P.Stenmark,C.Arrowsmith,H.Berglund,R.Busam,R.Collins, A.Edwards,M.Ehn,S.Flodin,A.Flores,S.Graslund,M.Hammarstrom, B.M.Hallberg,L.Holmberg Schiavone,M.Hogbom,T.Karlberg,T.Kotenyova, P.Loppnau,A.Magnusdottir,P.Nilsson-Ehle,T.Nyman,D.Ogg,C.Persson, J.Sagemark,M.Sundstrom,J.Uppenberg,A.G.Thorsell,S.Van Den Berg, J.Weigelt,M.Welin,P.Nordlund

Key ref:

K.Walldén et al. (2007). Crystal structure of human cytosolic 5'-nucleotidase II: insights into allosteric regulation and substrate recognition. J Biol Chem, 282, 17828-17836. PubMed id: 17405878 DOI: 10.1074/jbc.M700917200

Date:

16-Aug-06 Release date: 19-Sep-06

Protein chain

P49902  (5NTC_HUMAN) -  Cytosolic purine 5'-nucleotidase from Homo sapiens

Seq: 561 a.a.

Struc: 470 a.a.

Enzyme reactions

• Enzyme class 2: E.C.2.7.1.77 - nucleoside phosphotransferase.
• Reaction: a 2'-deoxyribonucleoside + a ribonucleoside 5'-phosphate = a ribonucleoside + a 2'-deoxyribonucleoside 5'-phosphate

2'-deoxyribonucleoside + ribonucleoside 5'-phosphate = ribonucleoside + 2'-deoxyribonucleoside 5'-phosphate (Bound ligand (Het Group name = GOL) matches with 60.00% similarity)

• Enzyme class 3: E.C.3.1.3.5 - 5'-nucleotidase.
• Reaction: a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate

ribonucleoside 5'-phosphate + H2O = ribonucleoside (Bound ligand (Het Group name = GOL) matches with 60.00% similarity) + phosphate

• Enzyme class 4: E.C.3.1.3.99 - IMP-specific 5'-nucleotidase.
• Reaction: IMP + H2O = inosine + phosphate
• Cofactor: Divalent metal cation

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1074/jbc.M700917200

J Biol Chem 282:17828-17836 (2007)

PubMed id: 17405878

Crystal structure of human cytosolic 5'-nucleotidase II: insights into allosteric regulation and substrate recognition.

K.Walldén, P.Stenmark, T.Nyman, S.Flodin, S.Gräslund, P.Loppnau, V.Bianchi, P.Nordlund.

ABSTRACT

Cytosolic 5'-nucleotidase II catalyzes the dephosphorylation of 6-hydroxypurine nucleoside 5'-monophosphates and regulates the IMP and GMP pools within the cell. It possesses phosphotransferase activity and thereby also catalyzes the reverse reaction. Both reactions are allosterically activated by adenine-based nucleotides and 2,3-bisphosphoglycerate. We have solved structures of cytosolic 5'-nucleotidase II as native protein (2.2 Angstrom) and in complex with adenosine (1.5 Angstrom) and beryllium trifluoride (2.15 Angstrom) The tetrameric enzyme is structurally similar to enzymes of the haloacid dehalogenase (HAD) superfamily, including mitochondrial 5'(3')-deoxyribonucleotidase and cytosolic 5'-nucleotidase III but possesses additional regulatory regions that contain two allosteric effector sites. At effector site 1 located near a subunit interface we modeled diadenosine tetraphosphate with one adenosine moiety in each subunit. This efficiently glues the tetramer subunits together in pairs. The model shows why diadenosine tetraphosphate but not diadenosine triphosphate activates the enzyme and supports a role for cN-II during apoptosis when the level of diadenosine tetraphosphate increases. We have also modeled 2,3-bisphosphoglycerate in effector site 1 using one phosphate site from each subunit. By comparing the structure of cytosolic 5'-nucleotidase II with that of mitochondrial 5'(3')-deoxyribonucleotidase in complex with dGMP, we identified residues involved in substrate recognition.

Selected figure(s)

Figure 5.
FIGURE 5. Effector sites 1 and 2 of cN-II with bound adenosine and sulfate. Omit F[o] - F[c] maps are covering adenosine with level of 4.5 in effector site 1 and level of 3 in effector site 2. A, stereo image of adenosine bound in effector site 1, with adenosine and amino acid residues colored in turquoise. B, stereo image of effector site 1 from two adjacent subunits connected through interface A. Salt bridges are indicated by the dotted lines. Nitrogens are shown in blue, oxygens in red, and sulfur in yellow. C, stereo image of adenosine bound in effector site 2. Note that the ribose moiety is disordered so that the electron density cannot confirm its location. Waters are colored in red. Polar atoms are color-coded as following: nitrogen in blue, oxygens in red, and sulfur in yellow.

Figure 7.
FIGURE 7. Two subunits of the tetrameric cN-II with three positively charged regions (K(25)KYRR), (K(359)SKKRQ), and (Q(420)RRIKK) shown in orange. Adenosines (white), sulfates (yellow and red), and magnesium (yellow) are also shown. Nitrogens are shown in blue and oxygens in red. The C-terminal end of the structure (residue 488) is marked C.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 17828-17836) copyright 2007.

Figures were selected by an automated process.