The　Holliday　junction　(HJ)　is　a　key　intermediate　during　homologous　recombination　and　DNA　double-strand　break　repair.　Timely　HJ　resolution　by　resolvases　is　critical　for　maintaining　genome　stability.　The　mechanisms　underlying　sequence-specific　substrate　recognition　and　cleavage　by　resolvases　remain　elusive.　The　monokaryotic　chloroplast　1　protein　(MOC1)　specifically　cleaves　four-way　DNA　junctions　in　a　sequence-specific　manner.　Here,　we　report　the　crystal　structures　of　MOC1　from　Zea　mays,　alone　or　bound　to　HJ　DNA.　MOC1　uses　a　unique　β-hairpin　to　embrace　the　DNA　junction.　A　base-recognition　motif　specifically　interacts　with　the　junction　center,　inducing　base　flipping　and　pseudobase-pair　formation　at　the　strand-exchanging　points.　Structures　of　MOC1　bound　to　HJ　and　different　metal　ions　support　a　two-metal　ion　catalysis　mechanism.　Further　molecular　dynamics　simulations　and　biochemical　analyses　reveal　a　communication　between　specific　substrate　recognition　and　metal　ion-dependent　catalysis.　Our　study　thus　provides　a　mechanism　for　how　a　resolvase　turns　substrate　specificity　into　catalytic　efficiency.　©　2019,　The　Author(s),　under　exclusive　licence　to　Springer　Nature　America,　Inc.