HEADER TRANSFERASE 16-DEC-05 2FEW
TITLE COMPLEX OF ENZYME IIAMTL AND PHOSPHORYLATED ENZYME IIBMTL FROM
TITLE 2 ESCHERICHIA COLI NMR, RESTRAINED REGULARIZED MEAN STRUCTURE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PTS SYSTEM MANNITOL-SPECIFIC EIICBA COMPONENT;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: EIIA-MTL, PHOSPHOTRANSFERASE ENZYME II, A DOMAIN COMPONENT;
COMPND 5 EC: 2.7.1.69;
COMPND 6 ENGINEERED: YES;
COMPND 7 MUTATION: YES;
COMPND 8 MOL_ID: 2;
COMPND 9 MOLECULE: MANNITOL-SPECIFIC PTS SYSTEM ENZYME IIABC COMPONENTS;
COMPND 10 CHAIN: B;
COMPND 11 FRAGMENT: EIIB-MTL, PHOSPHOTRANSFERASE ENZYME II, B DOMAIN COMPONENT;
COMPND 12 EC: 2.7.1.69;
COMPND 13 ENGINEERED: YES;
COMPND 14 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 562;
SOURCE 4 STRAIN: GI698;
SOURCE 5 GENE: MTLA;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 MOL_ID: 2;
SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O157:H7;
SOURCE 10 ORGANISM_TAXID: 83334;
SOURCE 11 STRAIN: GI698;
SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS PHOSPHOTRANSFERASE, TRANSFERASE, KINASE, SUGAR TRANSPORT, COMPLEX
KEYWDS 2 (TRANSFERASE-PHOSPHOCARRIER)
EXPDTA SOLUTION NMR
AUTHOR G.M.CLORE,J.Y.SUH
REVDAT 4 20-OCT-21 2FEW 1 REMARK SEQADV LINK
REVDAT 3 24-FEB-09 2FEW 1 VERSN
REVDAT 2 25-APR-06 2FEW 1 JRNL
REVDAT 1 07-FEB-06 2FEW 0
JRNL AUTH J.Y.SUH,M.CAI,D.C.WILLIAMS JR.,G.M.CLORE
JRNL TITL SOLUTION STRUCTURE OF A POST-TRANSITION STATE ANALOG OF THE
JRNL TITL 2 PHOSPHOTRANSFER REACTION BETWEEN THE A AND B CYTOPLASMIC
JRNL TITL 3 DOMAINS OF THE MANNITOL TRANSPORTER IIMANNITOL OF THE
JRNL TITL 4 ESCHERICHIA COLI PHOSPHOTRANSFERASE SYSTEM
JRNL REF J.BIOL.CHEM. V. 281 8939 2006
JRNL REFN ISSN 0021-9258
JRNL PMID 16443929
JRNL DOI 10.1074/JBC.M513466200
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : XPLOR-NIH
REMARK 3 AUTHORS : SCHWIETERS,KUSZEWSKI,TJANDRA,CLORE
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURES WERE CALCULATED BY CONJOINED RIGID BODY/TORSION
REMARK 3 ANGLE DYNAMICS (SCHWIETERS & CLORE (2001) J.MAGN.RESON 152, 288-
REMARK 3 302) THE TARGET FUNCTIONS COMPRISES TERMS FOR THE EXPERIMENTAL NOE
REMARK 3 RESTRAINTS AND SIDECHAIN TORSION ANGLE RESTRAINTS; A QUARTIC VAN
REMARK 3 DER WAALS REPULSION TERM (NILGES ET AL. (1988) FEBS LETT. 229, 129-
REMARK 3 136); A MULTIIMENSIONAL TORSION ANGLE DATABASE POTENTIAL OF MEAN
REMARK 3 FORCE (CLORE & KUSZEWSKI (2002) J.AM.CHEM.SOC. 124, 2866-2867);
REMARK 3 AND A RADIUS OF GYRATION POTENTIAL (KUSZEWSKI ET AL (1999)
REMARK 3 J.AM.CHEM.SOC. 121, 2337-2338). THE STARTING COORDINATES OF
REMARK 3 PHOSPHOIIBMTL ARE TAKEN FROM THE NMR STRUCTURE ((PDB ACCESSION
REMARK 3 CODE 1VRV, SUH ET AL. (2005) J.MOL.BIOL. 353, 1129-1136). THE
REMARK 3 STARTING STRUCTURE FOR IIAMTL IS TAKEN FROM THE COORDINATES OF
REMARK 3 IIAMTL IN THE IIAMTL-HPR COMPLEX (PDB ACCESSION CODE 1J6T;
REMARK 3 CORNILESCU ET AL. (2002) J.BIOL.CHEM. 277,42289-42298). THE
REMARK 3 COORDINATES OF IIAMTL IN THIS COMPLEX ARE DERIVED FROM MOLECULE D
REMARK 3 OF THE 1.8A RESOLUTION CRYSTAL STRUCTURE OF IIAMTL PDB ACCESSION
REMARK 3 CODE 1A3A, VAN MONTFORT ET AL. STRUCTURE 5, 217-225 (1998)). IN
REMARK 3 THE STRUCTURE DETERMINATION OF THE IIAMTL-PHOSPHOIIBMTL COMPLEX,
REMARK 3 THE BACKBONE COORDINATES AND NON-INTERFACIAL SIDECHAINS ARE
REMARK 3 TREATED AS RIGID BODIES THROUGHOUT WITH IIAMTL HELD FIXED AND
REMARK 3 PHOSPHOIIBMTL ALLOWED TO ROTATE AND TRANSLATE. THE INTERFACIAL
REMARK 3 SIDECHAINS ARE GIVEN FULL TORSIONAL DEGREES OF FREEDOM.
REMARK 3
REMARK 3 IN THIS ENTRY THE LAST COLUMN REPRESENTS THE AVERAGE RMS
REMARK 3 DIFFERENCE BETWEEN THE INDIVIDUAL SIMULATED ANNEALING
REMARK 3 STRUCTURES (TOTAL OF 200) AND THE MEAN COORDINATE POSITIONS. IT
REMARK 3 IS IMPORTANT TO NOTE THAT THE VALUES GIVEN FOR THE BACKBONE
REMARK 3 ATOMS AND NON-INTERFACIAL SIDECHAINS PROVIDE ONLY A
REMARK 3 MEASURE OF THE PRECISION WITH WHICH THE RELATIVE
REMARK 3 OF THE TWO PROTEINS HAVE BEEN DETERMINED AND DOES
REMARK 3 NOT TAKE INTO ACCOUNT THE ERRORS IN THE NMR COORDINATES
REMARK 3 OF PHOSPHOIIBMTL AND THE XRAY/NMR COORDINATES OF IIAMTL.
REMARK 3
REMARK 3 THE COORDINATES DEPOSITED CORRESPOND TO THE RESTRAINED
REMARK 3 REGULARIZED MEAN COORDINATES. THE STRUCTURE IS BASED ON
REMARK 3 84 INTERMOLECULAR NOE RESTRAINTS BETWEEN IIAMTL AND IIBMTL;
REMARK 3 37 INTRAMOLECULAR NOE RESTRAINTS FOR IIAMTL AND 46
REMARK 3 46 INTRAMOLECULAR NOE RESTRAINTS FOR IIBMTL RELATED
REMARK 3 ONLY TO INTERFACIAL SIDECHAINS; AND 55 SIDECHAIN TORSION ANGLE
REMARK 3 RESTRAINTS (36 FOR IIAMTL AND 19 FOR IIBMTL) RELATED
REMARK 3 TO INTERFACIAL SIDECHAINS ONLY.
REMARK 3 DEVIATIONS FROM NOE DISTANCE RESTRAINTS: 0.009 A
REMARK 3 DEVIATIONS FROM SIDECHAIN TORSION ANGLE RESTRAINTS: 0.31 DEG
REMARK 3 DEVIATIONS FROM IDEALIZED GEOMETRY: BONDS 0.006A,
REMARK 3 ANGLES: 0.9 DEG, IMPROPER TORSIONS 1.3 DEG.
REMARK 4
REMARK 4 2FEW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-DEC-05.
REMARK 100 THE DEPOSITION ID IS D_1000035795.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 303.00
REMARK 210 PH : 7.4
REMARK 210 IONIC STRENGTH : 20 MM TRIS-D11
REMARK 210 PRESSURE : NULL
REMARK 210 SAMPLE CONTENTS : NULL
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 750 MHZ; 800
REMARK 210 MHZ
REMARK 210 SPECTROMETER MODEL : DMX500; DMX600; DRX600; DRX750;
REMARK 210 DRX800
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : NULL
REMARK 210 METHOD USED : CONJOINED RIGID BODY/TORSION
REMARK 210 ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : REGULARIZED MEAN STRUCTURE
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL
REMARK 210
REMARK 210 REMARK: THE FOLLOWING EXPERIMENTS WERE CONDUCTED: (1) TRIPLE
REMARK 210 RESONANCE FOR ASSIGNMENT OF PROTEINS; (2) QUANTITATIVE J
REMARK 210 CORRELATION FOR COUPLING CONSTANTS; (3) 3D AND 4D HETERONUCLEAR
REMARK 210 SEPARATED AND FILTERED NOE EXPERIMENTS; (4) IPAP EXPERIMENTS FOR
REMARK 210 DIPOLAR COUPLINGS. DIPOLAR COUPLINGS WERE MEASURED IN A NEUTRAL
REMARK 210 AXIALLY STRETCHED POLYACRYLAMIDE GEL.
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, B
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 RES C SSSEQI
REMARK 465 MET A 1
REMARK 465 ALA A 2
REMARK 465 ASN A 3
REMARK 465 LYS A 148
REMARK 465 THR B 472
REMARK 465 GLU B 473
REMARK 465 ASN B 474
REMARK 465 GLU B 475
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME;
REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 470 RES CSSEQI ATOMS
REMARK 470 ARG A 147 O
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 HD1 HIS B 430 H ASP B 432 1.16
REMARK 500 HA LEU A 7 HD22 ASN A 11 1.26
REMARK 500 HH TYR A 42 H GLY A 66 1.30
REMARK 500 HG1 THR A 134 H SER A 136 1.31
REMARK 500 HH11 ARG A 99 HE2 HIS A 133 1.34
REMARK 500 HE ARG A 107 HD22 ASN A 108 1.35
REMARK 500 HE ARG A 107 ND2 ASN A 108 1.38
REMARK 500 HH22 ARG A 99 OE2 GLU A 129 1.39
REMARK 500 CD GLU A 41 HH21 ARG A 73 1.39
REMARK 500 O2P SEP B 384 H MET B 388 1.43
REMARK 500 O1P SEP B 384 H SER B 391 1.45
REMARK 500 OE2 GLU A 41 HH21 ARG A 73 1.51
REMARK 500 OE1 GLU A 41 HH21 ARG A 73 1.53
REMARK 500 OG SEP B 384 H GLY B 387 1.57
REMARK 500 OH TYR A 42 H GLY A 66 1.59
REMARK 500 OE1 GLU A 39 NH1 ARG A 73 1.88
REMARK 500 OE1 GLU A 41 NH2 ARG A 73 2.08
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 THR A 53 138.00 -172.46
REMARK 500 GLU A 110 32.15 -84.76
REMARK 500 ARG B 378 -3.03 -143.14
REMARK 500 ASP B 454 79.20 -61.94
REMARK 500
REMARK 500 REMARK: NULL
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 RESIDUE NUMBERING:
REMARK 999 IIAMTL: 4-147 (RESIDUES 1-3 ARE DISORDERED
REMARK 999 IN SOLUTION AND NOT VISIBLE IN THE ELECTRON DENSITY
REMARK 999 MAP OF THE CRYSTAL STRUCTURE OF THE FREE PROTEIN).
REMARK 999 IN INTACT ENZYME IIMTL, THESE COORESPOND TO
REMARK 999 RESIDUES 493-636 OF INTACT ENZYME IIMTL.
REMARK 999 IIBMTL: 375-471 (CORRESPONDS TO NUMBERING IN INTACT IIMTL)
REMARK 999 PHOSPHATE: RESIDUE 200
DBREF 2FEW A 2 148 UNP P00550 PTM3C_ECOLI 491 637
DBREF 2FEW B 375 475 GB 13363950 BAB37898 375 475
SEQADV 2FEW MET A 1 UNP P00550 INITIATING METHIONINE
SEQADV 2FEW GLN A 65 UNP P00550 HIS 554 ENGINEERED MUTATION
SEQADV 2FEW SEP B 384 GB 13363950 CYS 384 ENGINEERED MUTATION
SEQRES 1 A 148 MET ALA ASN LEU PHE LYS LEU GLY ALA GLU ASN ILE PHE
SEQRES 2 A 148 LEU GLY ARG LYS ALA ALA THR LYS GLU GLU ALA ILE ARG
SEQRES 3 A 148 PHE ALA GLY GLU GLN LEU VAL LYS GLY GLY TYR VAL GLU
SEQRES 4 A 148 PRO GLU TYR VAL GLN ALA MET LEU ASP ARG GLU LYS LEU
SEQRES 5 A 148 THR PRO THR TYR LEU GLY GLU SER ILE ALA VAL PRO GLN
SEQRES 6 A 148 GLY THR VAL GLU ALA LYS ASP ARG VAL LEU LYS THR GLY
SEQRES 7 A 148 VAL VAL PHE CYS GLN TYR PRO GLU GLY VAL ARG PHE GLY
SEQRES 8 A 148 GLU GLU GLU ASP ASP ILE ALA ARG LEU VAL ILE GLY ILE
SEQRES 9 A 148 ALA ALA ARG ASN ASN GLU HIS ILE GLN VAL ILE THR SER
SEQRES 10 A 148 LEU THR ASN ALA LEU ASP ASP GLU SER VAL ILE GLU ARG
SEQRES 11 A 148 LEU ALA HIS THR THR SER VAL ASP GLU VAL LEU GLU LEU
SEQRES 12 A 148 LEU ALA GLY ARG LYS
SEQRES 1 B 101 SER HIS VAL ARG LYS ILE ILE VAL ALA SEP ASP ALA GLY
SEQRES 2 B 101 MET GLY SER SER ALA MET GLY ALA GLY VAL LEU ARG LYS
SEQRES 3 B 101 LYS ILE GLN ASP ALA GLY LEU SER GLN ILE SER VAL THR
SEQRES 4 B 101 ASN SER ALA ILE ASN ASN LEU PRO PRO ASP VAL ASP LEU
SEQRES 5 B 101 VAL ILE THR HIS ARG ASP LEU THR GLU ARG ALA MET ARG
SEQRES 6 B 101 GLN VAL PRO GLN ALA GLN HIS ILE SER LEU THR ASN PHE
SEQRES 7 B 101 LEU ASP SER GLY LEU TYR THR SER LEU THR GLU ARG LEU
SEQRES 8 B 101 VAL ALA ALA GLN ARG HIS THR GLU ASN GLU
MODRES 2FEW SEP B 384 SER PHOSPHOSERINE
HET SEP B 384 14
HETNAM SEP PHOSPHOSERINE
HETSYN SEP PHOSPHONOSERINE
FORMUL 2 SEP C3 H8 N O6 P
HELIX 1 1 GLY A 8 GLU A 10 5 3
HELIX 2 2 THR A 20 GLY A 35 1 16
HELIX 3 3 GLU A 41 THR A 53 1 13
HELIX 4 4 THR A 67 VAL A 74 5 8
HELIX 5 5 ALA A 106 ASN A 109 5 4
HELIX 6 6 GLU A 110 LEU A 122 1 13
HELIX 7 7 ASP A 124 THR A 134 1 11
HELIX 8 8 SER A 136 ALA A 145 1 10
HELIX 9 9 GLY B 389 ALA B 405 1 17
HELIX 10 10 ARG B 431 VAL B 441 1 11
HELIX 11 11 ASP B 454 HIS B 471 1 18
SHEET 1 A 4 ILE A 12 PHE A 13 0
SHEET 2 A 4 GLY A 78 ARG A 89 1 O GLN A 83 N PHE A 13
SHEET 3 A 4 ILE A 97 ALA A 105 -1 O ARG A 99 N TYR A 84
SHEET 4 A 4 ILE A 61 ALA A 62 1 N ALA A 62 O ILE A 102
SHEET 1 B 4 SER B 411 ALA B 416 0
SHEET 2 B 4 LYS B 379 SEP B 384 1 N VAL B 382 O SER B 415
SHEET 3 B 4 LEU B 426 HIS B 430 1 O ILE B 428 N ILE B 381
SHEET 4 B 4 GLN B 445 LEU B 449 1 O GLN B 445 N VAL B 427
LINK C ALA B 383 N SEP B 384 1555 1555 1.33
LINK C SEP B 384 N ASP B 385 1555 1555 1.33
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
(ATOM LINES ARE NOT SHOWN.)
END
