HEADER TRANSCRIPTION REGULATOR 01-FEB-05 2BJC
TITLE NMR STRUCTURE OF A PROTEIN-DNA COMPLEX OF AN ALTERED SPECIFICITY
TITLE 2 MUTANT OF THE LAC REPRESSOR HEADPIECE THAT MIMICS THE GAL REPRESSOR
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LACTOSE OPERON REPRESSOR;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: DNA BINDING DOMAIN, LAC HEADPIECE RESIDUES 1-62;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES;
COMPND 7 OTHER_DETAILS: THE PROTEIN IS A DIMER. DISULFIDE BOND BETWEEN CYS52
COMPND 8 IN TWO MONOMERS FORMS A COVALENT DIMER;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: 5'-D(*GP*AP*AP*TP*TP*GP*TP*AP*AP*GP
COMPND 11 *CP*GP*CP*TP*TP*AP*CP*AP*AP*TP*TP*C)-3';
COMPND 12 CHAIN: C, D;
COMPND 13 SYNONYM: LAC-GAL OPERATOR;
COMPND 14 ENGINEERED: YES;
COMPND 15 OTHER_DETAILS: ALTERED LAC SYML OPERATOR
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 STRAIN: DH9;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_STRAIN: DH9;
SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET3A / PGP1-2;
SOURCE 9 MOL_ID: 2;
SOURCE 10 SYNTHETIC: YES
KEYWDS TRANSCRIPTION REGULATOR, SYMMETRIC DNA-BINDING, DNA-BINDING, HTH, LAC
KEYWDS 2 OPERON, LAC REPRESSOR, ALTERED SPECIFICITY, MUTANT, REPRESSOR,
KEYWDS 3 TRANSCRIPTION REGULATION, TRANSCRIPTION REGULATOR/DNA, GAL
KEYWDS 4 REPRESSOR, GAL OPERON, LAC HEADPIECE, SYMMETRIC DIMER
EXPDTA SOLUTION NMR
NUMMDL 16
AUTHOR R.K.SALINAS,G.E.FOLKERS,A.M.J.J.BONVIN,D.DAS,R.BOELENS,R.KAPTEIN
REVDAT 3 15-JAN-20 2BJC 1 REMARK
REVDAT 2 24-FEB-09 2BJC 1 VERSN
REVDAT 1 18-OCT-05 2BJC 0
JRNL AUTH R.K.SALINAS,G.E.FOLKERS,A.M.J.J.BONVIN,D.DAS,R.BOELENS,
JRNL AUTH 2 R.KAPTEIN
JRNL TITL ALTERED SPECIFICITY IN DNA BINDING BY THE LAC REPRESSOR: A
JRNL TITL 2 MUTANT LAC HEADPIECE THAT MIMICS THE GAL REPRESSOR
JRNL REF CHEMBIOCHEM V. 6 1628 2005
JRNL REFN ISSN 1439-4227
JRNL PMID 16094693
JRNL DOI 10.1002/CBIC.200500049
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH C.G.KALODIMOS,A.M.J.J.BONVIN,R.K.SALINAS,R.WECHSELBERGER,
REMARK 1 AUTH 2 R.BOELENS,R.KAPTEIN
REMARK 1 TITL PLASTICITY IN PROTEIN-DNA RECOGNITION: LAC REPRESSOR
REMARK 1 TITL 2 INTERACTS WITH ITS NATURAL OPERATOR O1 THROUGH ALTERNATIVE
REMARK 1 TITL 3 CONFORMATIONS OF ITS DNA BINDING DOMAIN
REMARK 1 REF EMBO J. V. 21 2866 2002
REMARK 1 REFN ISSN 0261-4189
REMARK 1 PMID 12065400
REMARK 1 DOI 10.1093/EMBOJ/CDF318
REMARK 1 REFERENCE 2
REMARK 1 AUTH N.LEHMING,J.SARTORIUS,M.NIEMOLER,G.GENENGER,
REMARK 1 AUTH 2 B.WILCKEN-BERGMANN,B.MULLER-HILL
REMARK 1 TITL THE INTERACTION OF THE RECOGNITION HELIX OF LAC REPRESSOR
REMARK 1 TITL 2 WITH LAC OPERATOR
REMARK 1 REF EMBO J. V. 6 3145 1987
REMARK 1 REFN ISSN 0261-4189
REMARK 1 PMID 2826131
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE-
REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,
REMARK 3 SIMONSON,WARREN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE
REMARK 3 JRNL CITATION ABOVE
REMARK 4
REMARK 4 2BJC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-FEB-05.
REMARK 100 THE DEPOSITION ID IS D_1290022790.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 315.0
REMARK 210 PH : 6.0
REMARK 210 IONIC STRENGTH : 20
REMARK 210 PRESSURE : 1.0 ATM
REMARK 210 SAMPLE CONTENTS : 95% WATER/5% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 15N NOESY-HSQC 3D 13C NOESY
REMARK 210 -HSQC 2D NOESY 2D NOESY WITH X-
REMARK 210 FILTERS 3D CBCACONH 3D HNCO 3D
REMARK 210 HBHACONH 3D HCCCONH 3D HCCH-
REMARK 210 TOCSY 2D 1H-13C HSQC 2D 1H-15N
REMARK 210 HSQC 2D 1H-15N J- MODULATED HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ
REMARK 210 SPECTROMETER MODEL : DMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : CNS
REMARK 210 METHOD USED : HADDOCK
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 50
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16
REMARK 210 CONFORMERS, SELECTION CRITERIA : RMSD TO AVERAGE STRUCTURE AND
REMARK 210 LOWEST ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3
REMARK 210
REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE RESONANCE NMR
REMARK 210 SPECTROSCOPY ON A 13C, 15N LABELED PROTEIN AND UNLABELED DNA.
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: TETRAMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D
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 ENGINEERED RESIDUES TYR 17 VAL, GLN 18 ALA AND VAL 52
REMARK 400 CYS IN CHAINS A AND B
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 H21 DG C 10 O2 DC D 113 1.47
REMARK 500 O2 DC C 13 H21 DG D 110 1.49
REMARK 500 O4 DT C 7 H61 DA D 116 1.59
REMARK 500 O2 DC C 22 H21 DG D 101 1.60
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 PRO A 3 -161.83 -76.13
REMARK 500 1 ALA A 27 -80.06 21.16
REMARK 500 1 SER A 28 -84.04 64.82
REMARK 500 1 ASN A 46 63.55 75.55
REMARK 500 1 PRO B 103 -164.53 -78.23
REMARK 500 1 VAL B 115 -168.26 -44.81
REMARK 500 1 ALA B 127 -79.69 21.30
REMARK 500 1 SER B 128 -84.22 66.02
REMARK 500 1 ASN B 146 65.43 78.03
REMARK 500 2 LYS A 2 86.61 -167.79
REMARK 500 2 PRO A 3 -167.27 -79.44
REMARK 500 2 GLN A 26 59.92 70.29
REMARK 500 2 ALA A 27 -72.11 4.54
REMARK 500 2 SER A 28 -77.40 63.16
REMARK 500 2 SER A 31 156.69 97.17
REMARK 500 2 ASN A 46 61.31 75.39
REMARK 500 2 SER A 61 -64.04 -152.08
REMARK 500 2 LYS B 102 87.21 -165.26
REMARK 500 2 PRO B 103 -167.28 -79.55
REMARK 500 2 GLN B 126 60.25 69.18
REMARK 500 2 ALA B 127 -71.08 7.07
REMARK 500 2 SER B 128 -80.89 63.96
REMARK 500 2 SER B 131 156.86 95.94
REMARK 500 2 ASN B 146 63.25 74.49
REMARK 500 2 SER B 161 -62.11 -151.94
REMARK 500 3 VAL A 15 -167.06 -45.34
REMARK 500 3 ALA A 27 -92.28 33.87
REMARK 500 3 SER A 28 -37.50 72.28
REMARK 500 3 ASN A 46 64.67 74.98
REMARK 500 3 LYS A 59 50.50 -109.08
REMARK 500 3 GLN A 60 -77.13 -61.99
REMARK 500 3 ALA B 127 -92.26 32.30
REMARK 500 3 SER B 128 -38.87 71.01
REMARK 500 3 ASN B 146 63.09 75.09
REMARK 500 3 LYS B 159 52.43 -105.29
REMARK 500 3 GLN B 160 -73.07 -63.40
REMARK 500 4 ALA A 27 -87.07 26.45
REMARK 500 4 SER A 28 -83.25 70.26
REMARK 500 4 HIS A 29 35.01 -83.63
REMARK 500 4 ASN A 46 62.03 72.58
REMARK 500 4 SER A 61 -67.35 -146.58
REMARK 500 4 GLN B 126 -25.85 99.81
REMARK 500 4 ALA B 127 -70.83 105.53
REMARK 500 4 SER B 128 -89.66 56.01
REMARK 500 4 ASN B 146 64.06 73.19
REMARK 500 4 SER B 161 -71.08 -151.48
REMARK 500 5 PRO A 3 -174.91 -67.07
REMARK 500 5 GLN A 26 -38.84 94.69
REMARK 500 5 ALA A 27 112.59 58.08
REMARK 500 5 ASN A 46 71.82 82.91
REMARK 500
REMARK 500 THIS ENTRY HAS 187 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 650
REMARK 650 HELIX
REMARK 650 DETERMINATION METHOD: AUTHOR PROVIDED.
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1CJG RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF LAC REPRESSOR HP62- DEOXYRIBONUCLEIC ACID COMPLEX
REMARK 900 RELATED ID: 1EFA RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF THE LAC REPRESSOR DIMER BOUND TO OPERATOR AND
REMARK 900 THE ANTI-INDUCER ONPF
REMARK 900 RELATED ID: 1JWL RELATED DB: PDB
REMARK 900 STRUCTURE OF THE DIMERIC LAC REPRESSOR/ OPERATOR O1/ONPFCOMPLEX
REMARK 900 RELATED ID: 1JYE RELATED DB: PDB
REMARK 900 STRUCTURE OF A DIMERIC LAC REPRESSOR WITH C-TERMINALDELETION AND
REMARK 900 K84L SUBSTITUTION
REMARK 900 RELATED ID: 1JYF RELATED DB: PDB
REMARK 900 STRUCTURE OF THE DIMERIC LAC REPRESSOR WITH AN 11-RESIDUE C-
REMARK 900 TERMINAL DELETION.
REMARK 900 RELATED ID: 1L1M RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF A DIMER OF LAC REPRESSOR DNA-BINDINGDOMAIN
REMARK 900 COMPLEXED TO ITS NATURAL OPERATOR O1
REMARK 900 RELATED ID: 1LBG RELATED DB: PDB
REMARK 900 LACTOSE OPERON REPRESSOR BOUND TO 21-BASE PAIR SYMMETRIC OPERATOR
REMARK 900 DEOXYRIBONUCLEIC ACID, ALPHA CARBONS ONLY
REMARK 900 RELATED ID: 1LBH RELATED DB: PDB
REMARK 900 INTACT LACTOSE OPERON REPRESSOR WITH GRATUITOUS INDUCER IPTG
REMARK 900 RELATED ID: 1LBI RELATED DB: PDB
REMARK 900 LAC REPRESSOR
REMARK 900 RELATED ID: 1LCC RELATED DB: PDB
REMARK 900 LAC REPRESSOR ("HEADPIECE") COMPLEX WITH AN 11 BASE-PAIR HALF-
REMARK 900 OPERATOR CORRESPONDING TO THE LEFT HALF OF THE WILD TYPE LAC
REMARK 900 OPERATOR (NMR, BEST STRUCTURE)
REMARK 900 RELATED ID: 1LCD RELATED DB: PDB
REMARK 900 LAC REPRESSOR ("HEADPIECE") COMPLEX WITH AN 11 BASE-PAIR HALF-
REMARK 900 OPERATOR CORRESPONDING TO THE LEFT HALF OF THE WILD TYPE LAC
REMARK 900 OPERATOR (NMR, 3 STRUCTURES)
REMARK 900 RELATED ID: 1LQC RELATED DB: PDB
REMARK 900 LAC REPRESSOR HEADPIECE (RESIDUES 1-56), NMR, 32 STRUCTURES
REMARK 900 RELATED ID: 1LTP RELATED DB: PDB
REMARK 900 RELATED ID: 1OSL RELATED DB: PDB
REMARK 900 SOLUTION STRUCTURE OF A DIMERIC LACTOSE DNA -BINDING
REMARK 900 DOMAINCOMPLEXED TO A NONSPECIFIC DNA SEQUENCE
REMARK 900 RELATED ID: 1TLF RELATED DB: PDB
REMARK 900 TRYPTIC CORE FRAGMENT OF THE LACTOSE REPRESSOR OF ESCHERICHIA COLI
REMARK 900 RELATED ID: 7354 RELATED DB: BMRB
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 RESIDUES 1-62 OF LAC REPRESSOR (P03023) WITH THE
REMARK 999 SUBSTITUTIONS Y17V Q18A AND V52C
REMARK 999 ALTERED PALINDROME OF THE LEFT SIDE OF THE LAC OPERATOR O1
REMARK 999 LACKING THE CENTRAL BASE PAIR.ORIGINAL BASE PAIR GC7 WAS
REMARK 999 SUBSTITUTED BY AT
DBREF 2BJC A 1 62 UNP P03023 LACI_ECOLI 1 62
DBREF 2BJC B 101 162 UNP P03023 LACI_ECOLI 1 62
DBREF 2BJC C 1 22 PDB 2BJC 2BJC 1 22
DBREF 2BJC D 101 122 PDB 2BJC 2BJC 101 122
SEQADV 2BJC VAL A 17 UNP P03023 TYR 17 ENGINEERED MUTATION
SEQADV 2BJC ALA A 18 UNP P03023 GLN 18 ENGINEERED MUTATION
SEQADV 2BJC CYS A 52 UNP P03023 VAL 52 ENGINEERED MUTATION
SEQADV 2BJC VAL B 117 UNP P03023 TYR 17 ENGINEERED MUTATION
SEQADV 2BJC ALA B 118 UNP P03023 GLN 18 ENGINEERED MUTATION
SEQADV 2BJC CYS B 152 UNP P03023 VAL 52 ENGINEERED MUTATION
SEQRES 1 A 62 MET LYS PRO VAL THR LEU TYR ASP VAL ALA GLU TYR ALA
SEQRES 2 A 62 GLY VAL SER VAL ALA THR VAL SER ARG VAL VAL ASN GLN
SEQRES 3 A 62 ALA SER HIS VAL SER ALA LYS THR ARG GLU LYS VAL GLU
SEQRES 4 A 62 ALA ALA MET ALA GLU LEU ASN TYR ILE PRO ASN ARG CYS
SEQRES 5 A 62 ALA GLN GLN LEU ALA GLY LYS GLN SER LEU
SEQRES 1 B 62 MET LYS PRO VAL THR LEU TYR ASP VAL ALA GLU TYR ALA
SEQRES 2 B 62 GLY VAL SER VAL ALA THR VAL SER ARG VAL VAL ASN GLN
SEQRES 3 B 62 ALA SER HIS VAL SER ALA LYS THR ARG GLU LYS VAL GLU
SEQRES 4 B 62 ALA ALA MET ALA GLU LEU ASN TYR ILE PRO ASN ARG CYS
SEQRES 5 B 62 ALA GLN GLN LEU ALA GLY LYS GLN SER LEU
SEQRES 1 C 22 DG DA DA DT DT DG DT DA DA DG DC DG DC
SEQRES 2 C 22 DT DT DA DC DA DA DT DT DC
SEQRES 1 D 22 DG DA DA DT DT DG DT DA DA DG DC DG DC
SEQRES 2 D 22 DT DT DA DC DA DA DT DT DC
HELIX 1 1 THR A 5 ALA A 13 1 9
HELIX 2 2 VAL A 17 ASN A 25 1 9
HELIX 3 3 ALA A 32 LEU A 45 1 14
HELIX 4 4 ALA A 53 GLY A 58 1 6
HELIX 5 5 THR B 105 ALA B 113 1 9
HELIX 6 6 VAL B 117 ASN B 125 1 9
HELIX 7 7 ALA B 132 LEU B 145 1 14
HELIX 8 8 ALA B 153 GLY B 158 1 6
SSBOND 1 CYS A 52 CYS B 152 1555 1555 2.03
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
(ATOM LINES ARE NOT SHOWN.)
END
