HEADER TRANSFERASE 18-DEC-12 3ZGP TITLE NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D- TITLE 2 TRANSPEPTIDASE ACYLATED BY ERTAPENEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERFK/YBIS/YCFS/YNHG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN, RESIDUES 341-466; COMPND 5 SYNONYM: LDTFM-ERTAPENEM; COMPND 6 EC: 2.3.2.12; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: ERTAPENEM ANTIBIOTIC IS COVALENTLY LINKED TO THE COMPND 9 CYSTEINE OF THE ENZYME. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECIUM; SOURCE 3 ORGANISM_TAXID: 1352; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PETTEV KEYWDS TRANSFERASE, TRANSPEPTIDATION, PEPTIDOGLYCAN BIOSYNTHESIS, ANTIBIOTIC KEYWDS 2 RESISTANCE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.LECOQ,S.TRIBOULET,V.DUBEE,C.BOUGAULT,J.E.HUGONNET,M.ARTHUR, AUTHOR 2 J.P.SIMORRE REVDAT 5 14-JUN-23 3ZGP 1 REMARK LINK ATOM REVDAT 4 24-JAN-18 3ZGP 1 JRNL REMARK REVDAT 3 12-FEB-14 3ZGP 1 HEADER REMARK HET HETNAM REVDAT 3 2 1 HETSYN FORMUL LINK TER REVDAT 3 3 1 HETATM MODEL ENDMDL CONECT REVDAT 3 4 1 MASTER REVDAT 2 28-AUG-13 3ZGP 1 JRNL REVDAT 1 24-APR-13 3ZGP 0 JRNL AUTH L.LECOQ,S.TRIBOULET,V.DUBEE,C.BOUGAULT,J.E.HUGONNET, JRNL AUTH 2 M.ARTHUR,J.P.SIMORRE JRNL TITL THE STRUCTURE OF ENTEROCOCCUS FAECIUM L,D---TRANSPEPTIDASE JRNL TITL 2 ACYLATED BY ERTAPENEM PROVIDES INSIGHT INTO THE INACTIVATION JRNL TITL 3 MECHANISM. JRNL REF ACS CHEM.BIOL. V. 8 1140 2013 JRNL REFN ISSN 1554-8929 JRNL PMID 23574509 JRNL DOI 10.1021/CB4001603 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: NULL REMARK 4 REMARK 4 3ZGP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1290055175. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.4 REMARK 210 IONIC STRENGTH : 300 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 10% WATER/90% D2O; 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-15N-HSQC; 1H-13C-HSQC REMARK 210 CENTERED ON ALIPHATICS; 1H-15N- REMARK 210 HMQC DETECTING 2J; 3J COUPLINGS REMARK 210 IN HISTIDINES IMIDAZOLE RING; REMARK 210 HSQC DETECTING 1J COUPLING IN REMARK 210 HISTIDINES IMIDAZOLE RING; REMARK 210 HNCACB; HNCO; 3D-15N-NOESY-HSQC; REMARK 210 3D-13C-NOESY-HSQC CENTERED ON REMARK 210 ALIPHATICS; 1H-13C- HSQC REMARK 210 CENTERED ON AROMATICS; 3D-13C- REMARK 210 NOESY-HSQC CENTERED ON AROMATICS; REMARK 210 13C-15N-FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ; 950 MHZ REMARK 210 SPECTROMETER MODEL : DIRECT DRIVE; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : AGILENT; BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UNIO 10, TALOS, CCPNMR ANALYSIS REMARK 210 ANALYSIS REMARK 210 METHOD USED : ARIA2.3 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1700 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE 20 NMR STRUCTURES WERE DETERMINED USING TRIPLE- REMARK 210 RESONANCE NMR SPECTROSCOPY ON A 13C, 15N-LABELED LDTFM SAMPLE REMARK 210 INCUBATED WITH 1 EQUIVALENT OF ERTAPENEM ANTIBIOTIC. THESE REMARK 210 STRUCTURES WERE REFINED IN WATER WITHIN CNS ARIA. 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 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 OD2 ASP A 432 HE1 TRP A 434 1.56 REMARK 500 O LEU A 433 H ARG A 437 1.56 REMARK 500 H MET A 354 O THR A 366 1.58 REMARK 500 H PHE A 382 O VAL A 463 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 6 PHE A 454 CZ PHE A 454 CE2 0.119 REMARK 500 10 PHE A 454 CZ PHE A 454 CE2 0.116 REMARK 500 16 PHE A 454 CZ PHE A 454 CE2 0.125 REMARK 500 17 PHE A 454 CZ PHE A 454 CE2 0.127 REMARK 500 18 PHE A 454 CZ PHE A 454 CE2 0.121 REMARK 500 20 PHE A 454 CE1 PHE A 454 CZ -0.123 REMARK 500 20 PHE A 454 CZ PHE A 454 CE2 0.144 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 MET A 340 -166.55 57.23 REMARK 500 1 TYR A 344 158.39 174.61 REMARK 500 1 GLN A 352 63.86 28.80 REMARK 500 1 SER A 370 -168.08 -78.63 REMARK 500 1 ALA A 379 137.88 57.67 REMARK 500 1 ASP A 398 -7.58 -55.71 REMARK 500 1 PRO A 412 83.38 -68.24 REMARK 500 1 TRP A 415 -2.45 50.79 REMARK 500 1 VAL A 418 172.67 -56.86 REMARK 500 1 ASP A 432 102.98 -53.48 REMARK 500 1 HIS A 440 -121.44 35.13 REMARK 500 1 LYS A 459 103.03 -56.36 REMARK 500 2 MET A 340 -168.61 60.93 REMARK 500 2 GLU A 341 171.20 -58.73 REMARK 500 2 TYR A 344 158.09 174.64 REMARK 500 2 GLN A 352 61.15 34.79 REMARK 500 2 SER A 370 -168.83 -77.69 REMARK 500 2 ALA A 379 138.59 62.48 REMARK 500 2 PRO A 412 75.94 -66.92 REMARK 500 2 TRP A 415 -56.73 82.91 REMARK 500 2 VAL A 418 173.08 -56.19 REMARK 500 2 ASP A 432 101.89 -52.01 REMARK 500 2 HIS A 440 -120.65 34.18 REMARK 500 2 CYS A 442 -165.63 -103.62 REMARK 500 2 LYS A 459 102.99 -57.28 REMARK 500 3 MET A 340 -167.23 62.01 REMARK 500 3 TYR A 344 158.82 174.15 REMARK 500 3 GLN A 352 63.54 32.69 REMARK 500 3 SER A 370 -167.98 -79.42 REMARK 500 3 ALA A 379 138.05 61.49 REMARK 500 3 PRO A 412 73.76 -67.81 REMARK 500 3 TRP A 415 -0.99 52.14 REMARK 500 3 VAL A 418 172.33 -56.85 REMARK 500 3 ASP A 432 100.80 -52.57 REMARK 500 3 HIS A 440 -117.61 33.54 REMARK 500 3 CYS A 442 -166.56 -103.57 REMARK 500 3 LYS A 459 101.86 -59.34 REMARK 500 4 MET A 340 -172.15 60.97 REMARK 500 4 GLU A 341 -179.50 -63.92 REMARK 500 4 TYR A 344 159.70 173.02 REMARK 500 4 GLN A 352 61.27 32.93 REMARK 500 4 ALA A 379 138.52 59.49 REMARK 500 4 ASP A 390 47.66 39.51 REMARK 500 4 ASP A 398 -2.60 -58.70 REMARK 500 4 PRO A 412 76.14 -67.63 REMARK 500 4 TRP A 415 -67.29 82.80 REMARK 500 4 VAL A 418 172.81 -56.26 REMARK 500 4 ASP A 432 102.35 -51.47 REMARK 500 4 HIS A 440 -115.69 35.99 REMARK 500 4 LYS A 459 102.14 -55.96 REMARK 500 REMARK 500 THIS ENTRY HAS 252 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 4 TYR A 409 0.06 SIDE CHAIN REMARK 500 5 TYR A 356 0.09 SIDE CHAIN REMARK 500 5 TYR A 409 0.05 SIDE CHAIN REMARK 500 7 TYR A 356 0.09 SIDE CHAIN REMARK 500 7 TYR A 409 0.06 SIDE CHAIN REMARK 500 8 TYR A 356 0.09 SIDE CHAIN REMARK 500 8 TYR A 409 0.07 SIDE CHAIN REMARK 500 9 TYR A 409 0.05 SIDE CHAIN REMARK 500 11 TYR A 356 0.09 SIDE CHAIN REMARK 500 11 TYR A 409 0.06 SIDE CHAIN REMARK 500 12 TYR A 409 0.05 SIDE CHAIN REMARK 500 14 TYR A 356 0.09 SIDE CHAIN REMARK 500 14 TYR A 409 0.06 SIDE CHAIN REMARK 500 15 TYR A 409 0.06 SIDE CHAIN REMARK 500 16 TYR A 356 0.09 SIDE CHAIN REMARK 500 17 TYR A 356 0.09 SIDE CHAIN REMARK 500 18 TYR A 409 0.07 SIDE CHAIN REMARK 500 19 TYR A 409 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1RG A 130 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZG4 RELATED DB: PDB REMARK 900 NMR STRUCTURE OF THE CATALYTIC DOMAIN FROM E. FAECIUM L,D- REMARK 900 TRANSPEPTIDASE REMARK 900 RELATED ID: 18911 RELATED DB: BMRB DBREF 3ZGP A 341 466 UNP Q3Y185 Q3Y185_ENTFC 341 466 SEQADV 3ZGP GLY A 338 UNP Q3Y185 EXPRESSION TAG SEQADV 3ZGP HIS A 339 UNP Q3Y185 EXPRESSION TAG SEQADV 3ZGP MET A 340 UNP Q3Y185 EXPRESSION TAG SEQRES 1 A 129 GLY HIS MET GLU ASP THR TYR ILE GLU VAL ASP LEU GLU SEQRES 2 A 129 ASN GLN HIS MET TRP TYR TYR LYS ASP GLY LYS VAL ALA SEQRES 3 A 129 LEU GLU THR ASP ILE VAL SER GLY LYS PRO THR THR PRO SEQRES 4 A 129 THR PRO ALA GLY VAL PHE TYR VAL TRP ASN LYS GLU GLU SEQRES 5 A 129 ASP ALA THR LEU LYS GLY THR ASN ASP ASP GLY THR PRO SEQRES 6 A 129 TYR GLU SER PRO VAL ASN TYR TRP MET PRO ILE ASP TRP SEQRES 7 A 129 THR GLY VAL GLY ILE HIS ASP SER ASP TRP GLN PRO GLU SEQRES 8 A 129 TYR GLY GLY ASP LEU TRP LYS THR ARG GLY SER HIS GLY SEQRES 9 A 129 CYS ILE ASN THR PRO PRO SER VAL MET LYS GLU LEU PHE SEQRES 10 A 129 GLY MET VAL GLU LYS GLY THR PRO VAL LEU VAL PHE HET 1RG A 130 58 HETNAM 1RG (4R,5S)-3-({(3S,5S)-5-[(3-CARBOXYPHENYL) HETNAM 2 1RG CARBAMOYL]PYRROLIDIN-3-YL}SULFANYL)-5-[(1S,2R)-1- HETNAM 3 1RG FORMYL-2-HYDROXYPROPYL]-4-METHYL-4,5-DIHYDRO-1H- HETNAM 4 1RG PYRROLE-2-CARBOXYLIC ACID HETSYN 1RG ERTAPENEM, BOUND FORM PRE-ISOMERIZED FORMUL 2 1RG C22 H27 N3 O7 S HELIX 1 1 LEU A 433 GLY A 438 1 6 HELIX 2 2 PRO A 447 VAL A 457 1 11 SHEET 1 AA 3 THR A 343 ASP A 348 0 SHEET 2 AA 3 GLN A 352 LYS A 358 -1 O HIS A 353 N ASP A 348 SHEET 3 AA 3 LYS A 361 ASP A 367 -1 O LYS A 361 N LYS A 358 SHEET 1 AB 2 VAL A 381 VAL A 384 0 SHEET 2 AB 2 THR A 461 VAL A 465 -1 O VAL A 463 N PHE A 382 SHEET 1 AC 4 LYS A 387 GLU A 389 0 SHEET 2 AC 4 TYR A 409 PRO A 412 -1 O TRP A 410 N GLU A 388 SHEET 3 AC 4 ILE A 420 ASP A 422 -1 O ILE A 420 N MET A 411 SHEET 4 AC 4 ILE A 443 THR A 445 1 O ILE A 443 N HIS A 421 SHEET 1 AD 2 THR A 392 THR A 396 0 SHEET 2 AD 2 PRO A 402 PRO A 406 -1 O TYR A 403 N GLY A 395 LINK CAA 1RG A 130 SG CYS A 442 1555 1555 1.75 SITE 1 AC1 12 LEU A 393 THR A 396 ASN A 397 ASP A 398 SITE 2 AC1 12 GLY A 400 TYR A 403 TRP A 410 GLY A 417 SITE 3 AC1 12 VAL A 418 HIS A 440 GLY A 441 CYS A 442 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