The crystal structure of human adenylate kinase 6: An adenylate kinase localized to the cell nucleus Hui Ren*†‡, Liya Wang‡§, Matthew Bennett*‡, Yuhe Liang*, Xiaofeng Zheng†, Fei Lu¶, Lanfen Li*†, Jie Nan†, Ming Luo†ʈ, Staffan Eriksson§, Chuanmao Zhang¶, and Xiao-Dong Su*†** *National Laboratory of Protein Engineering and Plant Genetic Engineering and Departments of †Biochemistry and Molecular Biology and ¶Cell Biology and Genetics, College of Life Sciences, Peking University, Beijing 100871, China; §Department of Molecular Biosciences, Section of Veterinary Medical Biochemistry, Swedish University of Agricultural Sciences, Uppsala Biomedicinska Centrum, P.O. Box 575, SE-751 23 Uppsala, Sweden; and ʈDepartment of Microbiology, University of Alabama at Birmingham, Birmingham, AL, 35294 Edited by Pamela J. Bjorkman, California Institute of Technology, Pasadena, CA, and approved November 29, 2004 (received for review October 7, 2004) Adenylate kinases (AKs) play important roles in nucleotide metab- human AD-004 (also referred to as AK6) has been described in olism in all organisms and in cellular energetics by means of ref. 10. Crystals of AK6 were obtained at room temperature phosphotransfer networks in eukaryotes. The crystal structure of within 2 weeks from conditions containing 1.44 M Li2SO4 in a human AK named AK6 was determined by in-house sulfur 0.1M Hepes, pH 7.5, by using the hanging-drop vapor diffusion single-wavelength anomalous dispersion phasing methods and method. The crystals belong to the space group P61 with unit cell refined to 2.0-Å resolution with a free R factor of 21.8%. Sequence parameters a ϭ b ϭ 99.56 Å and c ϭ 57.19 Å. analyses revealed that human AK6 belongs to a distinct subfamily of AKs present in all eukaryotic organisms sequenced so far. Data Collection, Structure Determination, and Refinement. Diffrac- Enzymatic assays show that human AK6 has properties similar with tion data sets were collected on a Bruker Smart 6000 charge- other AKs, particularly with AK5. Fluorescence microscopy showed coupled device detector mounted with a Nonius FR591 x-ray that human AK6 is localized predominantly to the nucleus of HeLa generator and Cu rotating anode. The 2.0- and 2.6-Å resolution cells. The identification of a nuclear-localized AK sheds light on data sets were collected from the same crystal, which was flash nucleotide metabolism in the nucleus and the energetic commu- cooled to 100 K. An oscillation scan of 0.15° was used for both nication between mitochondria and nucleus by means of phos- data sets. All diffraction data were indexed and integrated by photransfer networks. using the Bruker on-line program suite PROTEUM. Scaling and PROSCALE ͉ ͉ ͉ merging of the data were performed with of the x-ray crystallography nuclear localization nucleotide metabolism on-line programs. phosphotransfer networks The sulfur sites were determined by the program SOLVE (11) with data from 20 to Ϸ3.0 Å. The initial phases and their figures ucleoside monophosphate kinases (NMPKs), which phos- of merit (FOM) were then input into RESOLVE for solvent Nphorylate nucleoside monophosphates or deoxynucleoside flattening and protein autotracing (12). RESOLVE automatically monophosphates, which produce nucleoside diphosphates or traced 113 residues with correct side chains, and the remainder deoxynucleoside diphosphates, play important roles in the main- of the structure was built manually by using the program tenance of intracellular nucleotide pools in all organisms. Ad- XTALVIEW (13). enylate kinases (AKs) (ATP:AMP phophotransferases, EC ␥ Refinement of the structure with CNS (14) involved steps of 2.7.4.3) catalyze the reversible transfer of the -phosphate group energy minimization, simulated annealing, and individual B from a phosphate donor (normally ATP) to AMP, releasing two factor refinement. Reference and model rebuilding with 3F Ϫ molecules of ADP (1). Besides crucial roles in homeostasis of o 2F and F Ϫ F electron density maps were made by using the adenine nucleotide metabolism, AKs are involved in cellular c o c program O (15). The program PROCHECK (16) was used to check energetics through complex phosphotransfer networks regulat- BIOCHEMISTRY the quality of the model. ing intracellular ATP-producing processes (2, 3). At present, five AK isoforms with different subcellular local- 3 ͞ ization and substrate specificity have been characterized in AK Activity Assays. Radio-labeled nucleotides [ H]AMP [24 mCi ϭ ␥ 32 ͞ mammalian tissues (4). In this work, we have identified a sixth mmol (1 Ci 37 GBq)] and [ - P]ATP (3,000 Ci mmol) were AK isoform through a characterization of the adrenal gland purchased from Amersham Pharmacia Biosciences. Other protein AD-004 gene as part of a structural genomics project nucleosides and nucleotides were purchased from Sigma. The involving human genes (5). AK activity of human AK6 was measured by radiochemical 3 The AD-004 gene was first identified in a gene expression methods either with [ H]AMP as substrate or by using a ␥ 32 profiling study of the human hypothalamus–pituitary–adrenal phosphoryl transfer assay with [ - P]ATP as substrate (17), axis (6) and has also appeared in analyses of genomic and cDNA with modifications as described below. Standard reaction mix- sequences (7, 8). The putative protein sequence for AD-004 ture contained 50 mM Tris⅐HCl (pH 8.0), 0.5 mg͞ml BSA, 5 mM 3 contains 172 residues with an expected molecular mass of 20 DTT, 5 mM MgCl2,[ H]AMP, and 50 ng of purified AK6 protein kDa. AD-004 shows low overall sequence identity with proteins in a total volume of 50 ␮l. The reaction was started by addition of known structures; however, in its N-terminal regions are of the protein, and 10-␮l aliquots were withdrawn at 0-, 10-, 20-, sequence motifs [most notably a Walker motif (9)] that are and 30-min intervals and spotted on DE-81 filter paper and characteristic of NMPKs. Through the work presented here, including crystal structure determination, enzymatic assays, and subcellular localization experiments, we show that AD-004 con- This paper was submitted directly (Track II) to the PNAS office. stitutes a AKs isoform that has been named human AK6, with Abbreviations: AK, adenylate kinase; NMPK, nucleoside monophosphate kinase; SAD, many characteristics that distinguish it from the other eukaryotic single-wavelength anomalous dispersion. AKs. Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID code 1RKB). Materials and Methods ‡H.R., L.W., and M.B. contributed equally to this work. Protein Purification and Crystallization. The preparation of protein **To whom correspondence should be addressed. E-mail: [email protected]. used for both enzymatic assays and crystallization trials of © 2005 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0407459102 PNAS ͉ January 11, 2005 ͉ vol. 102 ͉ no. 2 ͉ 303–308 Downloaded by guest on September 29, 2021 dried. The filters were washed three times with 50 mM formic Table 1. Data collection, phase determination, and acid͞5 mM ammonium formate and rinsed once with water; then refinement statistics ͞ the products were eluted with 0.1 M HCl 0.2 M KCl, and the SAD phasing (2.6 Å) Refinement (2.0 Å) radioactivity was determined in a liquid scintillation counter. Enzymatic activity was calculated based on the formation of Data collection statistics [3H]ADP in the reaction. Resolution range, Å 57–2.6 (2.70–2.60) 57–2.0 (2.04–2.0) ͞ ͞ ϭ ϭ ϭ Phosphoryl transfer assays were performed with 0.1 mM Space group unit cell P61 a b 99.56; c 57.23 [␥-32P]ATP as the phosphate donor and nonradioactive nucle- parameters, Å oside monophosphate as the substrate in the buffer described Unique reflections, n 9,954 (999) 21,969 (1,125) above. The reaction proceeded for 20 min at 37°C and was Rmerge,% 3.04 (7.48) 3.37 (20.65) stopped by heating at 70°C for 2 min. After a brief centrifugation, Completeness, % 98.34 (89.84) 99.7 (99.4) 1 ␮l of the supernatant was spotted on a polyethyleneimine- Redundancy 33.48 (11.16) 5.15 (2.37) cellulose plate (Merck). The plates were developed in 0.2 M I͞␴(I)* 29.44 (5.41) 15.15 (1.73) 3͞ NaH2PO4 and autoradiographed. Nonradioactive nucleoside Vmax,Å Da 3.93 3.93 monophosphates, diphosphates, and triphosphates were used as Molecules per a.u. 1 1 standards. Refinement statistics Test set for Rfree 1,071 (174) † ͞ ‡ ͞ Immunofluorescence Assays. An antiserum against AK6 was pre- Rfactor, % Rfree, % 20.3 21.8 pared by immunizing a rabbit with purified AK6 protein as Deviation from ideality follows. A New Zealand rabbit was immunized s.c. with 0.5 mg Bonds, Å 0.006 of recombinant protein in Freud complete adjuvant (1:1 vol͞vol) Angles, ° 1.2 at five sites. Booster injections were given at 15 and 25 days in Average B factors, Å2 30 Freund’s incomplete adjuvant (1:1 vol͞vol). Blood samples were No. of nonhydrogen atoms taken right before the immunization as negative control and test Protein 173 bleeds were performed 7 days after the third immunization, and Water 161 2Ϫ ϩ the sera were checked for its potency against AK6 by ELISA Other 5 SO4 ,3Li assays. The antiserum was obtained 11 days after the third Ramachandran plot booster immunization. statistics HeLa cells were incubated in a medium containing 10% FCS, Most favored regions, % 92.9 1% penicillin͞streptomycin, and 89% DMEM on a cover glass Allowed regions, % 7.1 in 35-mm dishes for 24 h before an immunofluorescence exper- Generously allowed 0 iment. Cells were fixed with 3.7% paraformaldehyde for 30 min regions at room temperature, then washed with PBS and permeablized Disallowed regions 0 with 0.2% Triton X-100 for 5 min on ice.