HEADER ANTIBIOTIC 16-MAR-04 1UZT OBSLTE 07-MAR-05 1UZT 1WCO TITLE THE PYROPHOSPHATE CAGE: THE STRUCTURE OF THE NISIN/LIPID II TITLE 2 COMPLEX PROVIDES A BLUEPRINT FOR NOVEL ANTIBIOTICS COMPND MOL_ID: 1; COMPND 2 MOLECULE: WATER SOLUBLE LIPID II (3LII); COMPND 3 CHAIN: L; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: 3-LIPID II (3LII) IS A SHORT CHAIN LIPID II COMPND 6 VARIANT WITH THREE TRANS-ISOPRENE REPEATS INSTEAD OF COMPND 7 ELEVEN. 3LII IS SEMI-CHEMICALLY SYNTHESIZED.; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: LANTIBIOTIC NISIN Z; COMPND 10 CHAIN: N SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS (SUBSP. CREMORIS); SOURCE 5 STRAIN: NIZO 22186 KEYWDS LANTIBIOTICS, PEPTIDOGLYCAN, PORE FORMATION, CELL WALL KEYWDS 2 PRECURSOR, ANTIBIOTIC EXPDTA NMR, 20 STRUCTURES AUTHOR S.-T.D.HSU,E.BREUKINK,E.TISCHENKO,M.A.G.LUTTERS,B.DE AUTHOR 2 KRUIJFF,R.KAPTEIN,A.M.J.J.BONVIN,N.A.J.VAN NULAND REVDAT 3 07-MAR-05 1UZT 1 OBSLTE REVDAT 2 16-SEP-04 1UZT 1 SOURCE REVDAT 1 09-SEP-04 1UZT 0 JRNL AUTH S.-T.D.HSU,E.BREUKINK,E.TISCHENKO,M.A.G.LUTTERS, JRNL AUTH 2 B.DE KRUIJFF,R.KAPTEIN,A.M.J.J.BONVIN, JRNL AUTH 3 N.A.J.VAN NULAND JRNL TITL THE NISIN/LIPID II COMPLEX REVEALS A PYROPHOSPHATE JRNL TITL 2 CAGE THAT PROVIDES A BLUEPRINT FOR NOVEL JRNL TITL 3 ANTIBIOTICS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.BREUKINK,H.E.VAN HEUSDEN,P.J.VOLLMERHAUS, REMARK 1 AUTH 2 E.SWIEZEWSKA,L.BRUNNER,S.WALKER,A.J.HECK, REMARK 1 AUTH 3 B.DE KRUIJFF REMARK 1 TITL LIPID II IS AN INTRINSIC COMPONENT OF THE PORE REMARK 1 TITL 2 INDUCED BY NISIN IN BACTERIAL MEMBRANES REMARK 1 REF J. BIOL. CHEM. V. 278 19898 2003 REMARK 1 REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.-T.D.HSU,E.BREUKINK,B.DE KRUIJFF,R.KAPTEIN, REMARK 1 AUTH 2 A.M.J.J.BONVIN,N.A.J.VAN NULAND REMARK 1 TITL MAPPING THE TARGETED MEMBRANE PORE FORMATION REMARK 1 TITL 2 MECHANISM BY SOLUTION NMR: THE NISIN Z AND LIPID REMARK 1 TITL 3 II INTERACTION IN SDS MICELLES REMARK 1 REF BIOCHEMISTRY V. 41 7670 2002 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER ET AL NUMBER OF NON-HYDROGEN ATOMS USED REMARK 3 IN REFINEMENT. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: J.LINGE,M.A.WILLIAMS, REMARK 3 C.A.E.M.SPRONK,A.M.J.J.BONVIN AND M.NILGES, REFINEMENT OF REMARK 3 PROTEIN STRUCTURES IN EXPLICIT SOLVENT. PROTEINS: STRUCT. REMARK 3 FUNCT. GENETICS 50, 496-506 (2003) THE ENSEMBLE OF STRUCTURES REMARK 3 IS SUPERIMPOSED ON THE CA OF NISIN RESIDUES 1-12 (CHAIN N) AND REMARK 3 THE HEAVY ATOMS OF MURNAC, PYROPHOSPHATE AND THE FIRST REMARK 3 ISOPRENE OF 3-LIPID II (CHAIN L) BECAUSE THESE ARE THE ONLY REMARK 3 SEGMENTS THAT HAVE SUFFICIENT DISTANCE RESTRAINTS TO DEFINE REMARK 3 THE COMPLEX STRUCTURE. OTHER RESIDUES, NAMELY RESIDUES 13-34 REMARK 3 (ESPECIALLY RESIDUES 20-34) OF NISIN AND THE PENTAPEPTIDE AND REMARK 3 TERMINAL ISOPRENE UNITS OF 3-LIPID II ARE FLEXIBLE AS REMARK 3 SUPPORTED BY DYNAMICS DATA. THE ATOM OCCUPANCY OF THE C- REMARK 3 TERMINAL TAIL OF NISIN (RESIDUES 20-34) HAS BEEN MODIFIED TO REMARK 3 BE 0.3, AS CRYSTALLOGRAPHERS DO FOR THE DISORDERED LOOPS WHICH REMARK 3 LACK ELECTRON DENSITY. REMARK 4 REMARK 4 1UZT COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY EBI ON 16-MAR-2004. REMARK 100 THE EBI ID CODE IS EBI-14809. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : DISSOLVED IN 100 D6-DMSO REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-15N-NOESY HSQC, 1H-1H REMARK 210 NOESY, 1H-15N TOCSY-HSQC, 1H- REMARK 210 1H TOCSY, 1H-1H COSY, 1H-13C REMARK 210 HSQC, 1H-13C HMBC, 31P-EDITED REMARK 210 1H-15N CT HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ, 600 MHZ, 750 MHZ, REMARK 210 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS/HADDOCK REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 6 REMARK 210 REMARK 210 REMARK: CLOSED TO AVERAGE. THE SOLUTION STRUCTURE OF NISIN/ REMARK 210 3LII COMPLEX WAS DETERMINED USING 15N-LABELLED NISIN AND REMARK 210 UNLABELLED 3LII BASED ON NOE RESTRAINTS, BACKBONE/SIDE CHAIN REMARK 210 TORSION RESTRAINTS AND EXPERIMENTALLY IDENTIFIED REMARK 210 INTERMOLECULAR HYDROGEN BONDS AS DISTANCE RESTRAINTS 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 1 ALA L 4 N 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 REMARK 500 CB ABA N 25 SG CYS N 28 1.81 REMARK 500 CB ABA N 8 SG CYS N 11 1.82 REMARK 500 CB ABA N 23 SG CYS N 26 1.82 REMARK 500 CB ABA N 13 SG CYS N 19 1.83 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 M RES CSSEQI PSI PHI REMARK 500 1 ABA N 8 -59.58 135.49 REMARK 500 1 MET N 21 -54.29 74.30 REMARK 500 1 ABA N 23 26.61 116.62 REMARK 500 1 DHA N 33 -51.39 79.99 REMARK 500 2 ABA N 8 -61.56 148.88 REMARK 500 2 MET N 21 -55.85 78.46 REMARK 500 2 DHA N 33 -54.47 85.88 REMARK 500 3 ABA N 8 -60.43 149.83 REMARK 500 3 DHA N 33 -54.80 82.25 REMARK 500 4 ABA N 8 -59.57 146.33 REMARK 500 4 ABA N 23 25.66 149.17 REMARK 500 4 DHA N 33 -59.55 73.77 REMARK 500 5 ABA N 8 -52.84 139.31 REMARK 500 5 MET N 21 -37.98 79.99 REMARK 500 5 DHA N 33 -57.39 95.10 REMARK 500 6 ABA N 8 -54.31 145.74 REMARK 500 6 MET N 21 -51.98 74.31 REMARK 500 6 ABA N 23 27.54 143.35 REMARK 500 6 DHA N 33 -61.99 85.16 REMARK 500 7 ABA N 8 -57.28 142.02 REMARK 500 7 ASN N 20 -45.24 72.42 REMARK 500 7 MET N 21 -42.98 74.76 REMARK 500 7 DHA N 33 -60.95 77.16 REMARK 500 8 ABA N 8 -56.35 145.40 REMARK 500 8 DHA N 33 -55.97 95.41 REMARK 500 9 ABA N 8 -53.49 140.64 REMARK 500 9 MET N 21 -49.66 74.71 REMARK 500 9 DHA N 33 -54.98 81.35 REMARK 500 10 ABA N 8 -59.44 147.20 REMARK 500 10 MET N 21 -46.84 73.75 REMARK 500 10 ABA N 23 26.20 141.83 REMARK 500 10 DHA N 33 -58.01 92.73 REMARK 500 11 ABA N 8 -54.05 142.41 REMARK 500 11 MET N 21 -56.90 73.93 REMARK 500 11 ABA N 23 24.99 116.16 REMARK 500 11 DHA N 33 -59.06 82.41 REMARK 500 12 ABA N 8 -54.62 143.45 REMARK 500 12 MET N 21 -35.90 71.19 REMARK 500 12 DHA N 33 -56.58 82.77 REMARK 500 13 ABA N 8 -59.40 149.10 REMARK 500 13 MET N 21 -53.57 72.72 REMARK 500 13 ABA N 23 37.25 142.61 REMARK 500 13 DHA N 33 -109.74 65.56 REMARK 500 14 ASN N 20 -56.11 74.85 REMARK 500 14 MET N 21 -57.95 72.17 REMARK 500 14 DHA N 33 -58.12 79.81 REMARK 500 15 ABA N 8 -57.09 140.71 REMARK 500 15 DHA N 33 -55.72 93.77 REMARK 500 16 ABA N 8 -58.97 145.68 REMARK 500 16 ABA N 23 -40.43 73.02 REMARK 500 16 DHA N 33 -55.32 77.00 REMARK 500 17 MET N 21 -32.89 71.02 REMARK 500 17 DHA N 33 -56.44 79.28 REMARK 500 18 ABA N 8 -48.87 129.40 REMARK 500 18 MET N 21 -47.60 74.94 REMARK 500 18 ABA N 23 22.46 123.99 REMARK 500 18 DHA N 33 -60.49 89.84 REMARK 500 19 ABA N 8 -53.01 144.25 REMARK 500 19 MET N 21 -47.56 73.54 REMARK 500 19 ABA N 23 -12.34 149.17 REMARK 500 19 DHA N 33 -54.73 80.78 REMARK 500 20 ABA N 8 -56.00 138.38 REMARK 500 20 MET N 21 -68.71 77.34 REMARK 500 20 DHA N 33 -50.92 79.88 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS THE PRECURSOR SEQUENCE WITH LEADER PEPTIDE BEFORE POST DBREF 1UZT L 1 5 PDB 1UZT 1UZT 1 5 DBREF 1UZT N 1 34 UNP P29559 LANZ_LACLA 24 57 SEQRES 1 L 5 ALA AA4 LYS ALA ALA SEQRES 1 N 34 ILE DBU DAL ILE DHA LEU CYS ABA PRO GLY CYS LYS ABA SEQRES 2 N 34 GLY ALA LEU MET GLY CYS ASN MET LYS ABA ALA ABA CYS SEQRES 3 N 34 ASN CYS SER ILE HIS VAL DHA LYS MODRES 1UZT DBU N 2 THR 3,4-DIHYDROXYBENZOIC ACID MODRES 1UZT DAL N 3 ALA D-ALANINE MODRES 1UZT DHA N 5 ALA 2- AMINO- ACRYLIC ACID MODRES 1UZT DHA N 33 ALA 2- AMINO- ACRYLIC ACID MODRES 1UZT AA4 L 2 ALA 2-AMINO-5-HYDROXYPENTANOIC ACID MODRES 1UZT ABA N 8 ALA ALPHA-AMINOBUTYRIC ACID MODRES 1UZT ABA N 13 ALA ALPHA-AMINOBUTYRIC ACID MODRES 1UZT ABA N 23 ALA ALPHA-AMINOBUTYRIC ACID MODRES 1UZT ABA N 25 ALA ALPHA-AMINOBUTYRIC ACID HET AA4 L 2 15 HET DBU N 2 11 HET DAL N 3 9 HET DHA N 5 8 HET ABA N 8 12 HET ABA N 13 12 HET ABA N 23 12 HET ABA N 25 12 HET DHA N 33 8 HET NAG L 6 28 HET MUB L 7 34 HET FPP L 8 49 HETNAM AA4 2-AMINO-5-HYDROXYPENTANOIC ACID HETNAM DBU (2E)-2-AMINOBUT-2-ENOIC ACID HETNAM DAL D-ALANINE HETNAM DHA 2-AMINO-ACRYLIC ACID HETNAM ABA ALPHA-AMINOBUTYRIC ACID HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM MUB N-ACETYLMURAMIC ACID HETNAM FPP FARNESYL DIPHOSPHATE HETSYN DBU Z-DEHYDROBUTYRINE HETSYN DHA 2,3-DIDEHYDROALANINE HETSYN NAG NAG FORMUL 1 AA4 C5 H11 N O3 FORMUL 2 DBU C4 H7 N O2 FORMUL 2 DAL C3 H7 N O2 FORMUL 2 DHA 2(C3 H5 N O2) FORMUL 2 ABA 4(C4 H9 N O2) FORMUL 3 NAG C8 H15 N O6 FORMUL 4 MUB C11 H19 N O8 FORMUL 5 FPP C15 H28 O7 P2 HELIX 1 1 ABA N 8 ABA N 13 5 6 LINK N ALA L 1 C10 MUB L 7 LINK C1 NAG L 6 O4 MUB L 7 LINK C1 MUB L 7 O1B FPP L 8 LINK C ILE N 1 N DBU N 2 LINK C DBU N 2 N DAL N 3 LINK CB DAL N 3 SG CYS N 7 LINK C DAL N 3 N ILE N 4 LINK C ILE N 4 N DHA N 5 LINK C DHA N 5 N LEU N 6 LINK C VAL N 32 N DHA N 33 LINK C DHA N 33 N LYS N 34 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