HEADER HYDROLASE 15-JAN-05 1YJT TITLE SOLUTION STRUCTURE OF THE CU(I) FORM OF THE SIXTH SOLUBLE DOMAIN A69P TITLE 2 MUTANT OF MENKES PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-TRANSPORTING ATPASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SIXTH SOLUBLE DOMAIN; COMPND 5 SYNONYM: COPPER PUMP 1, MENKES DISEASE-ASSOCIATED PROTEIN; COMPND 6 EC: 3.6.3.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ATP7A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET20B+ KEYWDS METALLOCHAPERONE, PROTEIN-PROTEIN INTERACTION, COPPER(I), METAL KEYWDS 2 HOMEOSTASIS, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR L.BANCI,I.BERTINI,F.CANTINI,M.MIGLIARDI,A.ROSATO,S.WANG REVDAT 4 29-MAY-24 1YJT 1 REMARK REVDAT 3 10-NOV-21 1YJT 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1YJT 1 VERSN REVDAT 1 03-JAN-06 1YJT 0 JRNL AUTH L.BANCI,I.BERTINI,F.CANTINI,M.MIGLIARDI,A.ROSATO,S.WANG JRNL TITL AN ATOMIC-LEVEL INVESTIGATION OF THE DISEASE-CAUSING A629P JRNL TITL 2 MUTANT OF THE MENKES PROTEIN, ATP7A JRNL REF J.MOL.BIOL. V. 352 409 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16083905 JRNL DOI 10.1016/J.JMB.2005.07.034 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, AMBER 5.0 REMARK 3 AUTHORS : REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH, REMARK 3 WEINER,KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE BASED ON A TOTAL OF REMARK 3 1901 MEANINGFUL DISTANCE CONSTRAINTS, 81 DIHEDRAL ANGLE REMARK 3 RESTRAINTS REMARK 4 REMARK 4 1YJT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031594. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100MM PHOSPHATE BUFFER REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8MM 15N LABELED SAMPLE; 5MM REMARK 210 DTT; 100MM PHOSPHATE BUFFER; REMARK 210 0.8MM 15N 13C LABELED SAMPLE; REMARK 210 5MM DTT; 100MM PHOSPHATE BUFFER; REMARK 210 1.0MM UNLABELED SAMPLE; 5MM DTT; REMARK 210 100MM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; CBCANH; REMARK 210 CBCACONH; HNCO; HNCACO; 2D NOESY; REMARK 210 2D TOCSY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.2, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS COUPLED REMARK 210 WITH SIMULATED ANNEALING REMARK 210 FOLLOWED BY RESTRAINED ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: MONOMERIC 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: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 21 GLU A 75 CA - C - O ANGL. DEV. = -39.4 DEGREES 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 THR A 14 25.46 -157.84 REMARK 500 1 THR A 27 72.75 -68.06 REMARK 500 1 LYS A 28 -38.88 -171.83 REMARK 500 1 ASN A 42 54.99 35.06 REMARK 500 1 PRO A 50 48.70 -81.48 REMARK 500 1 GLU A 51 -63.09 -137.29 REMARK 500 1 VAL A 72 -52.97 -140.40 REMARK 500 1 LYS A 73 81.17 57.42 REMARK 500 1 ILE A 74 -84.62 -73.84 REMARK 500 2 ASP A 3 170.71 61.64 REMARK 500 2 THR A 14 22.30 -153.34 REMARK 500 2 THR A 27 72.12 -65.49 REMARK 500 2 LYS A 28 -43.58 -150.52 REMARK 500 2 ARG A 30 -82.12 131.36 REMARK 500 2 ASN A 42 54.99 33.73 REMARK 500 2 PRO A 50 41.26 -77.84 REMARK 500 2 ILE A 52 -54.46 -132.12 REMARK 500 2 PRO A 69 80.79 -68.82 REMARK 500 2 LEU A 71 64.16 -68.50 REMARK 500 2 LYS A 73 136.07 68.27 REMARK 500 3 ASP A 3 -143.20 52.78 REMARK 500 3 GLU A 51 -68.63 -135.16 REMARK 500 3 VAL A 72 57.73 -102.71 REMARK 500 3 LYS A 73 -137.33 45.55 REMARK 500 4 THR A 14 41.91 -152.81 REMARK 500 4 HIS A 29 87.08 -68.48 REMARK 500 4 ARG A 30 -66.21 23.27 REMARK 500 4 PRO A 50 47.56 -80.63 REMARK 500 4 GLU A 51 -63.90 -134.16 REMARK 500 4 VAL A 72 -76.70 -81.28 REMARK 500 4 LYS A 73 150.31 67.62 REMARK 500 5 ASP A 3 75.16 35.01 REMARK 500 5 THR A 14 11.62 -155.22 REMARK 500 5 LYS A 28 -38.03 -169.91 REMARK 500 5 ASN A 42 41.81 79.24 REMARK 500 5 GLU A 51 25.66 -159.99 REMARK 500 5 ILE A 52 -50.70 -167.17 REMARK 500 5 VAL A 72 -43.36 -141.81 REMARK 500 5 LYS A 73 -123.90 42.83 REMARK 500 5 ILE A 74 -71.20 -91.49 REMARK 500 6 ASP A 3 162.89 63.00 REMARK 500 6 VAL A 5 61.86 -153.98 REMARK 500 6 THR A 14 10.85 -155.10 REMARK 500 6 THR A 27 75.84 -66.81 REMARK 500 6 LYS A 28 -40.02 179.64 REMARK 500 6 ASN A 42 47.02 34.78 REMARK 500 6 LYS A 73 -160.43 57.67 REMARK 500 7 ASP A 3 173.73 174.80 REMARK 500 7 LYS A 28 -30.83 -162.69 REMARK 500 7 ARG A 30 -85.60 139.59 REMARK 500 REMARK 500 THIS ENTRY HAS 192 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS A 35 SER A 36 1 140.33 REMARK 500 MET A 1 GLY A 2 2 -136.35 REMARK 500 CYS A 35 SER A 36 3 144.76 REMARK 500 HIS A 29 ARG A 30 4 145.39 REMARK 500 CYS A 35 SER A 36 5 142.04 REMARK 500 LYS A 43 ALA A 44 8 147.94 REMARK 500 ALA A 44 HIS A 45 8 148.79 REMARK 500 ILE A 74 GLU A 75 10 137.40 REMARK 500 CYS A 35 SER A 36 16 144.34 REMARK 500 MET A 1 GLY A 2 17 136.37 REMARK 500 CYS A 35 SER A 36 17 142.87 REMARK 500 CYS A 35 SER A 36 20 139.42 REMARK 500 MET A 1 GLY A 2 22 131.59 REMARK 500 MET A 1 GLY A 2 24 141.00 REMARK 500 ILE A 74 GLU A 75 26 135.79 REMARK 500 CYS A 35 SER A 36 29 141.83 REMARK 500 ALA A 44 HIS A 45 30 149.47 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 2 ARG A 11 0.11 SIDE CHAIN REMARK 500 2 TYR A 34 0.15 SIDE CHAIN REMARK 500 2 TYR A 48 0.10 SIDE CHAIN REMARK 500 3 ARG A 11 0.08 SIDE CHAIN REMARK 500 3 HIS A 29 0.09 SIDE CHAIN REMARK 500 3 TYR A 48 0.10 SIDE CHAIN REMARK 500 4 ARG A 30 0.12 SIDE CHAIN REMARK 500 5 ARG A 11 0.14 SIDE CHAIN REMARK 500 5 TYR A 48 0.08 SIDE CHAIN REMARK 500 6 HIS A 45 0.08 SIDE CHAIN REMARK 500 6 TYR A 48 0.07 SIDE CHAIN REMARK 500 7 TYR A 48 0.13 SIDE CHAIN REMARK 500 8 ARG A 11 0.10 SIDE CHAIN REMARK 500 8 ARG A 56 0.10 SIDE CHAIN REMARK 500 11 ARG A 56 0.09 SIDE CHAIN REMARK 500 12 TYR A 34 0.07 SIDE CHAIN REMARK 500 13 HIS A 29 0.09 SIDE CHAIN REMARK 500 14 HIS A 45 0.10 SIDE CHAIN REMARK 500 14 TYR A 48 0.12 SIDE CHAIN REMARK 500 15 HIS A 45 0.11 SIDE CHAIN REMARK 500 15 ARG A 56 0.12 SIDE CHAIN REMARK 500 17 TYR A 48 0.17 SIDE CHAIN REMARK 500 17 ARG A 56 0.13 SIDE CHAIN REMARK 500 18 ARG A 11 0.10 SIDE CHAIN REMARK 500 19 HIS A 45 0.09 SIDE CHAIN REMARK 500 19 TYR A 48 0.10 SIDE CHAIN REMARK 500 20 HIS A 45 0.10 SIDE CHAIN REMARK 500 20 TYR A 48 0.07 SIDE CHAIN REMARK 500 21 ARG A 11 0.08 SIDE CHAIN REMARK 500 21 TYR A 48 0.09 SIDE CHAIN REMARK 500 22 ARG A 56 0.15 SIDE CHAIN REMARK 500 23 ARG A 30 0.08 SIDE CHAIN REMARK 500 23 TYR A 48 0.20 SIDE CHAIN REMARK 500 24 HIS A 29 0.09 SIDE CHAIN REMARK 500 24 TYR A 34 0.12 SIDE CHAIN REMARK 500 24 HIS A 45 0.10 SIDE CHAIN REMARK 500 27 TYR A 48 0.08 SIDE CHAIN REMARK 500 28 TYR A 48 0.09 SIDE CHAIN REMARK 500 29 ARG A 56 0.10 SIDE CHAIN REMARK 500 30 TYR A 34 0.08 SIDE CHAIN REMARK 500 30 TYR A 48 0.07 SIDE CHAIN 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 CU1 A 76 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 15 SG REMARK 620 2 CYS A 18 SG 156.7 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU1 A 76 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YJR RELATED DB: PDB REMARK 900 THE APO FORM OF THE SAME PROTEIN, A69P MUTANT REMARK 900 RELATED ID: 1YJU RELATED DB: PDB REMARK 900 THE APO FORM OF THE SAME PROTEIN REMARK 900 RELATED ID: 1YJV RELATED DB: PDB REMARK 900 THE CU(I) FORM OF THE SAME PROTEIN DBREF 1YJT A 2 73 UNP Q04656 ATP7A_HUMAN 562 633 SEQADV 1YJT MET A 1 UNP Q04656 CLONING ARTIFACT SEQADV 1YJT PRO A 69 UNP Q04656 ALA 629 ENGINEERED MUTATION SEQADV 1YJT ILE A 74 UNP Q04656 CLONING ARTIFACT SEQADV 1YJT GLU A 75 UNP Q04656 CLONING ARTIFACT SEQRES 1 A 75 MET GLY ASP GLY VAL LEU GLU LEU VAL VAL ARG GLY MET SEQRES 2 A 75 THR CYS ALA SER CYS VAL HIS LYS ILE GLU SER SER LEU SEQRES 3 A 75 THR LYS HIS ARG GLY ILE LEU TYR CYS SER VAL ALA LEU SEQRES 4 A 75 ALA THR ASN LYS ALA HIS ILE LYS TYR ASP PRO GLU ILE SEQRES 5 A 75 ILE GLY PRO ARG ASP ILE ILE HIS THR ILE GLU SER LEU SEQRES 6 A 75 GLY PHE GLU PRO SER LEU VAL LYS ILE GLU HET CU1 A 76 1 HETNAM CU1 COPPER (I) ION FORMUL 2 CU1 CU 1+ HELIX 1 1 CYS A 15 THR A 27 1 13 HELIX 2 2 GLY A 54 SER A 64 1 11 SHEET 1 A 4 ILE A 32 ALA A 38 0 SHEET 2 A 4 LYS A 43 TYR A 48 -1 O LYS A 47 N TYR A 34 SHEET 3 A 4 LEU A 6 ARG A 11 -1 N LEU A 8 O ALA A 44 SHEET 4 A 4 GLU A 68 LEU A 71 -1 O SER A 70 N VAL A 9 LINK SG CYS A 15 CU CU1 A 76 1555 1555 2.15 LINK SG CYS A 18 CU CU1 A 76 1555 1555 2.15 SITE 1 AC1 2 CYS A 15 CYS A 18 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