Crystal structure of the 5'->3' exoribonuclease Xrn1, E178Q mutant

Structural and biochemical studies of the 5' -> 3' exoribonuclease Xrn1.

MGIPKFFHFISERWPQISQLIDGSQIPEFDNLYLDMNSILHNCTHGDGSEVNSRLSEEEVYSKIFSYIDHLFHTIKPKQT
FYMAIDGVAPRAKMNQQRARRFRTAMDAEKALQKAIENGDELPKGEPFDSNAITPGTEFMAKLTENLKYFIHDKITNDTR
WQNVKVIFSGHEVPGEGQHKIMDYIRAIRAQEDYNPNTRHCIYGLDADLIILGLSTHDHHFCLLREEVTFGKRSSSVKTL
ETQNFFLLHLSILREYLALEFEEITDSVQFEYDFERVLDDFIFVLFTIGNDFLPNLPDLHLKKGAFPVLLQTFKEALQHM
DGYINEQGKINLARFSIWLKYLSDFEYLNFEKKDIDVEWFNQQLENISLEGERKRTRMGKKLLMKQQKKLIGAVKPWLLK
TVQRKVTSELQDADFEIFPLEDKELVRANLDFLKEFAFDLGLILAHSKSKDLYYFKLDLDSIN(UNK)(UNK)(UNK)
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
IYSERFVEWKDQYYKDKLDFSINDTDSLKEMTENYVGGLQWVLYYYYRGCPSWSWYYRYHYAPRISDVIKGIDQNIEFHK
GQPFKPFQQLMAVLPERSKNLIPVVYRPLMYDEHSPILDFYPNEVELDLNGKTADWEAVVKISFVDQKRLVEAMAPYDAK
LSPDEKKRNSFGTDLIFIFNPQVDTVYKTPLAGLFNDIEHNHCIEREFIPESMENVKFLFGLPKGAKLGASSLAGFPSLK
TLPLTAELAYNSSVVFNFPSKQQSMVLHIQDLYKENGISLSDLAKRHMGKIVYSRWPFLRESKLLSLITEETVYEGVKSG
KLTKVIERKPQDFERKEFRELKMTLKSNYQRTKAILLDDISALAKVVPVNGLVRNSDGSYSKSFNETIEYYPLQLIVEDV
KNKDERYIEKEPLPINKEFPKGSKVVFLGDYAYGGEATVDGYNSETRLKLTVKKGSLRAEPNIGKVRAKLDSQALRFYPT
QV(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)
(UNK)(UNK)(UNK)(UNK)SSAEADSILKTVADWLSEARKPFVVVSLESDSLTKASMAAVESEIIKYVSLPDSSEQKKL
AKVPREAILNAESSYVLLRSQRFHLGDRVMYIQDSGKVPLHSKGTVVGYTSIGKNVSIQVLFDNEIIAGNNFGGRLQTRR
GLGLDSSFLLNLSDRQLVYHSKASLEHHHHHH

MGIPKFFHFISERWPQISQLIDGSQIPEFDNLYLDMNSILHNCTHGDGSEVNSRLSEEEVYSKIFSYIDHLFHTIKPKQT
FYMAIDGVAPRAKMNQQRARRFRTAMDAEKALQKAIENGDELPKGEPFDSNAITPGTEFMAKLTENLKYFIHDKITNDTR
WQNVKVIFSGHEVPGEGQHKIMDYIRAIRAQEDYNPNTRHCIYGLDADLIILGLSTHDHHFCLLREEVTFGKRSSSVKTL
ETQNFFLLHLSILREYLALEFEEITDSVQFEYDFERVLDDFIFVLFTIGNDFLPNLPDLHLKKGAFPVLLQTFKEALQHM
DGYINEQGKINLARFSIWLKYLSDFEYLNFEKKDIDVEWFNQQLENISLEGERKRTRMGKKLLMKQQKKLIGAVKPWLLK
TVQRKVTSELQDADFEIFPLEDKELVRANLDFLKEFAFDLGLILAHSKSKDLYYFKLDLDSINXXXXXXXXXXXXXXXXX
XXIYSERFVEWKDQYYKDKLDFSINDTDSLKEMTENYVGGLQWVLYYYYRGCPSWSWYYRYHYAPRISDVIKGIDQNIEF
HKGQPFKPFQQLMAVLPERSKNLIPVVYRPLMYDEHSPILDFYPNEVELDLNGKTADWEAVVKISFVDQKRLVEAMAPYD
AKLSPDEKKRNSFGTDLIFIFNPQVDTVYKTPLAGLFNDIEHNHCIEREFIPESMENVKFLFGLPKGAKLGASSLAGFPS
LKTLPLTAELAYNSSVVFNFPSKQQSMVLHIQDLYKENGISLSDLAKRHMGKIVYSRWPFLRESKLLSLITEETVYEGVK
SGKLTKVIERKPQDFERKEFRELKMTLKSNYQRTKAILLDDISALAKVVPVNGLVRNSDGSYSKSFNETIEYYPLQLIVE
DVKNKDERYIEKEPLPINKEFPKGSKVVFLGDYAYGGEATVDGYNSETRLKLTVKKGSLRAEPNIGKVRAKLDSQALRFY
PTQVXXXXXXXXXXXXXXXXXXXSSAEADSILKTVADWLSEARKPFVVVSLESDSLTKASMAAVESEIIKYVSLPDSSEQ
KKLAKVPREAILNAESSYVLLRSQRFHLGDRVMYIQDSGKVPLHSKGTVVGYTSIGKNVSIQVLFDNEIIAGNNFGGRLQ
TRRGLGLDSSFLLNLSDRQLVYHSKASLEHHHHHH

0.1M Tris, 0.9M LiCl, 13.5% PEG 6000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

E178Q IS AN ACTIVE SITE MUTATION. AMINO ACID SEQUENCE CORRESPONDING TO RESIDUES 1-1245 IN UNIPROT DATABASE ENTRY Q6CJ09, PLUS A C-TERMINAL EXPRESSION TAG (RESIDUES 1246-1253), WAS USED FOR CRYSTALLIZATION. MOST OF THE RESIDUES FROM RESIDUE 463 TO 503, AND FROM RESIDUE 984 TO 1082 WERE MISSING IN THE COORDINATES DUE TO LACK OF ELECTRON DENSITY. SEVERAL RESIDUES WITHIN THESE RANGES WERE MODELED AS POLY-ALA SEGMENTS, AND ARE REPRESENTED AS UNK RESIDUES 469-487 AND 1038-1052 OF CHAIN A, UNK RESIDUES 469-487 AND 1036-1052 OF CHAIN B, UNK RESIDUES 469-487 AND 1038-1054 OF CHAIN C, AND UNK RESIDUES 469-487 OF CHAIN D. THESE RESIDUE NUMBERS ARE ARBITRARILY ASSIGNED. IT IS EXPECTED THAT RESIDUES 469-487 BELONG TO THE 463-503 SEGMENT, AND RESIDUES 1036-1054 BELONG TO THE 984-1082 SEGMENT.

HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Beta berrel, Tudor domain, Chromo domain, mRNA turnover, rRNA processing, RNA binding, DNA binding, HYDROLASE

MGIPKFFHFISERWPQISQLIDGSQIPEFDNLYLDMNSILHNCTHGDGSEVNSRLSEEEVYSKIFSYIDHLFHTIKPKQT
FYMAIDGVAPRAKMNQQRARRFRTAMDAEKALQKAIENGDELPKGEPFDSNAITPGTEFMAKLTENLKYFIHDKITNDTR
WQNVKVIFSGHEVPGEGEHKIMDYIRAIRAQEDYNPNTRHCIYGLDADLIILGLSTHDHHFCLLREEVTFGKRSSSVKTL
ETQNFFLLHLSILREYLALEFEEITDSVQFEYDFERVLDDFIFVLFTIGNDFLPNLPDLHLKKGAFPVLLQTFKEALQHM
DGYINEQGKINLARFSIWLKYLSDFEYLNFEKKDIDVEWFNQQLENISLEGERKRTRMGKKLLMKQQKKLIGAVKPWLLK
TVQRKVTSELQDADFEIFPLEDKELVRANLDFLKEFAFDLGLILAHSKSKDLYYFKLDLDSIN

IYSERFVEWKDQYYKDKLDFSINDTDSLKEMTENYVGGLQWVLYYYYRGCPSWSWYYRYHYAPRISDVIKGIDQNIEFHK
GQPFKPFQQLMAVLPERSKNLIPVVYRPLMYDEHSPILDFYPNEVELDLNGKTADWEAVVKISFVDQKRLVEAMAPYDAK
LSPDEKKRNSFGTDLIFIFNPQVDTVYKTPLAGLFNDIEHNHCIEREFIPESMENVKFLFGLPKGAKLGASSLAGFPSLK
TLPLTAELAYNSSVVFNFPSKQQSMVLHIQDLYKENGISLSDLAKRHMGKIVYSRWPFLRESKLLSLITEETVYEGVKSG
KLTKVIERKPQDFERKEFRELKMTLKSNYQRTKAILLDDISALAKVVPVNGLVRNSDGSYSKSFNETIEYYPLQLIVEDV
KNKDERYIEKEPLPINKEFPKGSKVVFLGDYAYGGEATVDGYNSETRLKLTVKKGSLRAEPNIGKVRAKLDSQALRFYPT
QV

SSAEADSILKTVADWLSEARKPFVVVSLESDSLTKASMAAVESEIIKYVSLPDSSEQKKLAKVPREAILNAESSYVLLRS
QRFHLGDRVMYIQDSGKVPLHSKGTVVGYTSIGKNVSIQVLFDNEIIAGNNFGGRLQTRRGLGLDSSFLLNLSDRQLVYH
SKAS