HEADER HYDROLASE/HYDROLASE INHIBITOR 01-MAY-09 2KID TITLE SOLUTION STRUCTURE OF THE S. AUREUS SORTASE A-SUBSTRATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: SORTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 62-206; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: (PHQ)LPA(B27) PEPTIDE; COMPND 8 CHAIN: C; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 1280; SOURCE 4 GENE: SRTA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET9A; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: SYNTHESIZED SUBSTRATE THAT MIMICS THE LPXTG MOTIF SOURCE 13 (NATIVE) SUBSTRATE KEYWDS SORTASE, EIGHT STRANDED BETA BARREL, TRANSPEPTIDASE, ENZYME-SUBSTRATE KEYWDS 2 COMPLEX, HYDROLASE-HYDROLASE INHIBITOR COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR N.SUREE,C.K.LIEW,V.A.VILLAREAL,W.THIEU,E.A.FADEEV,J.J.CLEMENS, AUTHOR 2 M.E.JUNG,R.T.CLUBB REVDAT 5 15-NOV-23 2KID 1 REMARK LINK ATOM REVDAT 4 26-FEB-20 2KID 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2KID 1 VERSN REVDAT 2 06-OCT-09 2KID 1 JRNL REVDAT 1 21-JUL-09 2KID 0 JRNL AUTH N.SUREE,C.K.LIEW,V.A.VILLAREAL,W.THIEU,E.A.FADEEV, JRNL AUTH 2 J.J.CLEMENS,M.E.JUNG,R.T.CLUBB JRNL TITL THE STRUCTURE OF THE STAPHYLOCOCCUS AUREUS SORTASE-SUBSTRATE JRNL TITL 2 COMPLEX REVEALS HOW THE UNIVERSALLY CONSERVED LPXTG SORTING JRNL TITL 3 SIGNAL IS RECOGNIZED. JRNL REF J.BIOL.CHEM. V. 284 24465 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19592495 JRNL DOI 10.1074/JBC.M109.022624 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, PROCHECKNMR REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. (X-PLOR NIH), LASKOWSKI AND REMARK 3 MACARTHUR (PROCHECKNMR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SOFTWARE USED: PIPP, NMRPIPE, REMARK 3 ATNOS/CANDID, REFINEMENT: RESIDUAL DIPOLAR COUPLINGS (RDC) REMARK 4 REMARK 4 2KID COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000101157. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 302 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-100% 13C; U-100% 15N] REMARK 210 SORTASE A, 1 MM CBZ-LPAT*, 50 MM REMARK 210 TRIS, 100 MM SODIUM CHLORIDE, 20 REMARK 210 MM CALCIUM CHLORIDE, 0.01 % REMARK 210 SODIUM AZIDE, 93 % H2O, 7 % [U- REMARK 210 100% 2H] D2O, 93% H2O, 7% D2O; 1 REMARK 210 MM [U-100% 15N] SORTASE A, 1 MM REMARK 210 CBZ-LPAT*, 50 MM TRIS, 100 MM REMARK 210 SODIUM CHLORIDE, 20 MM CALCIUM REMARK 210 CHLORIDE, 0.01 % SODIUM AZIDE, REMARK 210 93 % H2O, 7 % [U-100% 2H] D2O, REMARK 210 93% H2O, 7% D2O; 1 MM [U-100% REMARK 210 13C; U-100% 15N] SORTASE A, 1 MM REMARK 210 CBZ-LPAT*, 50 MM TRIS, 100 MM REMARK 210 SODIUM CHLORIDE, 20 MM CALCIUM REMARK 210 CHLORIDE, 0.01 % SODIUM AZIDE, REMARK 210 100 % [U-100% 2H] D2O, 93% H2O, REMARK 210 7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-15N TOCSY; REMARK 210 3D 1H-13C NOESY; 3D CBCA(CO)NH; REMARK 210 3D C(CO)NH; 3D HNCO; 3D HNCACB; REMARK 210 3D HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HNHA; 3D HNHB; 3D HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP, NMRPIPE, NMRDRAW, MOLMOL, REMARK 210 SPARKY, ATNOS/CANDID REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE (PHQ)LPA(B27) PEPTIDE IS PEPTIDE-LIKE, A MEMBER OF INHIBITOR REMARK 400 CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: (PHQ)LPA(B27) PEPTIDE REMARK 400 CHAIN: C REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASP A 68 H LYS A 71 1.36 REMARK 500 O LYS A 137 HG SER A 140 1.42 REMARK 500 O GLU A 95 HD21 ASN A 98 1.44 REMARK 500 O LEU A 110 HH12 ARG A 151 1.44 REMARK 500 H LEU A 181 O PHE A 200 1.49 REMARK 500 H ALA A 73 O VAL A 87 1.51 REMARK 500 H TYR A 75 O LYS A 145 1.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ILE A 65 106.37 -46.27 REMARK 500 1 LYS A 69 -14.57 -45.45 REMARK 500 1 ALA A 92 32.26 -71.83 REMARK 500 1 LEU A 97 -6.56 -49.31 REMARK 500 1 VAL A 101 103.75 -51.49 REMARK 500 1 ALA A 104 -12.45 -45.23 REMARK 500 1 ASN A 107 35.45 -79.05 REMARK 500 1 TYR A 128 -153.07 -68.17 REMARK 500 1 LYS A 134 -17.78 -45.37 REMARK 500 1 LYS A 138 177.77 -42.74 REMARK 500 1 MET A 155 109.04 -45.94 REMARK 500 1 LYS A 162 171.23 -44.05 REMARK 500 1 PRO A 163 32.24 -77.89 REMARK 500 1 THR A 164 -2.84 -152.26 REMARK 500 1 LEU A 169 -13.59 -49.83 REMARK 500 1 ASP A 170 90.97 19.46 REMARK 500 1 GLN A 172 -52.12 -128.73 REMARK 500 1 LYS A 177 -176.01 -45.07 REMARK 500 1 ASP A 185 -152.86 -165.68 REMARK 500 1 PRO C 703 -160.79 -51.34 REMARK 500 1 ALA C 704 98.39 51.03 REMARK 500 2 ILE A 65 103.78 -42.18 REMARK 500 2 PRO A 66 -159.99 -87.36 REMARK 500 2 ASP A 68 48.62 -76.79 REMARK 500 2 LYS A 69 -13.25 -49.30 REMARK 500 2 ALA A 92 30.57 -72.78 REMARK 500 2 LEU A 97 -7.82 -49.52 REMARK 500 2 VAL A 101 108.30 -59.94 REMARK 500 2 ASN A 107 32.84 -77.05 REMARK 500 2 LEU A 110 -3.26 -59.81 REMARK 500 2 TYR A 128 -150.52 -75.30 REMARK 500 2 GLN A 129 -89.10 -68.10 REMARK 500 2 LYS A 134 -18.21 -43.00 REMARK 500 2 LYS A 138 178.27 -43.17 REMARK 500 2 MET A 155 107.33 -45.87 REMARK 500 2 LYS A 162 170.38 -47.36 REMARK 500 2 PRO A 163 37.32 -78.00 REMARK 500 2 THR A 164 -7.98 -152.19 REMARK 500 2 VAL A 166 -30.00 -39.77 REMARK 500 2 LEU A 169 -9.40 -47.54 REMARK 500 2 ASP A 170 27.86 35.60 REMARK 500 2 GLU A 171 94.56 -69.34 REMARK 500 2 GLN A 172 -74.06 -155.14 REMARK 500 2 LYS A 175 -76.90 -36.89 REMARK 500 2 LYS A 177 178.01 -40.50 REMARK 500 2 ASP A 185 -153.92 -165.87 REMARK 500 2 PRO C 703 -179.19 -69.59 REMARK 500 2 ALA C 704 -171.30 45.05 REMARK 500 3 GLN A 60 -177.41 -61.01 REMARK 500 3 ILE A 65 99.30 -37.83 REMARK 500 REMARK 500 THIS ENTRY HAS 474 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 700 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 105 OE2 REMARK 620 2 GLU A 108 OE2 66.2 REMARK 620 3 ASP A 112 OD2 147.7 101.0 REMARK 620 4 ASN A 114 O 113.4 59.5 80.0 REMARK 620 5 GLU A 171 OE1 68.5 134.7 117.6 145.5 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF (PHQ)LPA(B27) REMARK 800 PEPTIDE REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1IJA RELATED DB: PDB REMARK 900 STRUCTURE OF SORTASE, THE TRANSPEPTIDASE THAT ANCHORS PROTEINS TO REMARK 900 THE CELL WALL OF STAPHYLOCOCCUS AUREUS REMARK 900 RELATED ID: 1T2P RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURES OF STAPHYLOCOCCUS AUREUS SORTASE A AND ITS REMARK 900 SUBSTRATE COMPLEX REMARK 900 RELATED ID: 16270 RELATED DB: BMRB DBREF 2KID A 60 206 UNP Q9S446 Q9S446_STAAU 60 206 DBREF 2KID C 701 705 PDB 2KID 2KID 701 705 SEQADV 2KID MET A 59 UNP Q9S446 INITIATING METHIONINE SEQRES 1 A 148 MET GLN ALA LYS PRO GLN ILE PRO LYS ASP LYS SER LYS SEQRES 2 A 148 VAL ALA GLY TYR ILE GLU ILE PRO ASP ALA ASP ILE LYS SEQRES 3 A 148 GLU PRO VAL TYR PRO GLY PRO ALA THR PRO GLU GLN LEU SEQRES 4 A 148 ASN ARG GLY VAL SER PHE ALA GLU GLU ASN GLU SER LEU SEQRES 5 A 148 ASP ASP GLN ASN ILE SER ILE ALA GLY HIS THR PHE ILE SEQRES 6 A 148 ASP ARG PRO ASN TYR GLN PHE THR ASN LEU LYS ALA ALA SEQRES 7 A 148 LYS LYS GLY SER MET VAL TYR PHE LYS VAL GLY ASN GLU SEQRES 8 A 148 THR ARG LYS TYR LYS MET THR SER ILE ARG ASP VAL LYS SEQRES 9 A 148 PRO THR ASP VAL GLY VAL LEU ASP GLU GLN LYS GLY LYS SEQRES 10 A 148 ASP LYS GLN LEU THR LEU ILE THR CYS ASP ASP TYR ASN SEQRES 11 A 148 GLU LYS THR GLY VAL TRP GLU LYS ARG LYS ILE PHE VAL SEQRES 12 A 148 ALA THR GLU VAL LYS SEQRES 1 C 5 PHQ LEU PRO ALA B27 MODRES 2KID B27 C 705 THR (2R,3S) 3-AMINO-4-MERCAPTO-2-BUTANOL HET PHQ C 701 17 HET B27 C 705 16 HET CA A 700 1 HETNAM PHQ BENZYL CHLOROCARBONATE HETNAM B27 (2R,3S) 3-AMINO-4-MERCAPTO-2-BUTANOL HETNAM CA CALCIUM ION HETSYN B27 (2R,3S)-3-AMINO-4-SULFANYLBUTAN-2-OL FORMUL 2 PHQ C8 H7 CL O2 FORMUL 2 B27 C4 H11 N O S FORMUL 3 CA CA 2+ HELIX 1 1 THR A 93 ASN A 98 1 6 HELIX 2 2 ASN A 132 ALA A 136 5 5 HELIX 3 3 ASP A 165 ASP A 170 5 6 SHEET 1 A 8 ILE A 83 VAL A 87 0 SHEET 2 A 8 GLY A 74 ILE A 78 -1 N ILE A 76 O GLU A 85 SHEET 3 A 8 MET A 141 VAL A 146 -1 O LYS A 145 N TYR A 75 SHEET 4 A 8 GLU A 149 VAL A 161 -1 O TYR A 153 N VAL A 142 SHEET 5 A 8 ARG A 197 GLU A 204 -1 O THR A 203 N LYS A 154 SHEET 6 A 8 LEU A 181 CYS A 184 -1 N LEU A 181 O PHE A 200 SHEET 7 A 8 ILE A 117 GLY A 119 1 N ILE A 117 O ILE A 182 SHEET 8 A 8 SER A 102 PHE A 103 -1 N SER A 102 O ALA A 118 LINK SG CYS A 184 SG B27 C 705 1555 1555 2.02 LINK C1 PHQ C 701 N LEU C 702 1555 1555 1.31 LINK C ALA C 704 N B27 C 705 1555 1555 1.30 LINK OE2 GLU A 105 CA CA A 700 1555 1555 2.51 LINK OE2 GLU A 108 CA CA A 700 1555 1555 2.86 LINK OD2 ASP A 112 CA CA A 700 1555 1555 2.63 LINK O ASN A 114 CA CA A 700 1555 1555 2.51 LINK OE1 GLU A 171 CA CA A 700 1555 1555 2.84 CISPEP 1 GLY A 90 PRO A 91 1 0.19 CISPEP 2 GLY A 90 PRO A 91 2 -0.18 CISPEP 3 GLY A 90 PRO A 91 3 0.14 CISPEP 4 GLY A 90 PRO A 91 4 0.10 CISPEP 5 GLY A 90 PRO A 91 5 0.27 CISPEP 6 GLY A 90 PRO A 91 6 0.65 CISPEP 7 GLY A 90 PRO A 91 7 0.24 CISPEP 8 GLY A 90 PRO A 91 8 0.14 CISPEP 9 GLY A 90 PRO A 91 9 0.62 CISPEP 10 GLY A 90 PRO A 91 10 0.10 CISPEP 11 GLY A 90 PRO A 91 11 -0.26 CISPEP 12 GLY A 90 PRO A 91 12 0.13 CISPEP 13 GLY A 90 PRO A 91 13 0.65 CISPEP 14 GLY A 90 PRO A 91 14 0.13 CISPEP 15 GLY A 90 PRO A 91 15 0.17 CISPEP 16 GLY A 90 PRO A 91 16 -0.04 CISPEP 17 GLY A 90 PRO A 91 17 0.69 CISPEP 18 GLY A 90 PRO A 91 18 0.57 CISPEP 19 GLY A 90 PRO A 91 19 -0.24 CISPEP 20 GLY A 90 PRO A 91 20 0.17 SITE 1 AC1 5 GLU A 105 GLU A 108 ASP A 112 ASN A 114 SITE 2 AC1 5 GLU A 171 SITE 1 AC2 14 ALA A 92 ALA A 104 ALA A 118 GLY A 119 SITE 2 AC2 14 HIS A 120 LYS A 162 PRO A 163 THR A 164 SITE 3 AC2 14 ASP A 165 VAL A 166 VAL A 168 CYS A 184 SITE 4 AC2 14 TRP A 194 ARG A 197 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1