HEADER HYDROLASE 01-APR-08 2K2G TITLE SOLUTION STRUCTURE OF THE WILD-TYPE CATALYTIC DOMAIN OF HUMAN MATRIX TITLE 2 METALLOPROTEINASE 12 (MMP-12) IN COMPLEX WITH A TIGHT-BINDING TITLE 3 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROPHAGE METALLOELASTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (UNP RESIDUES 100 TO 263); COMPND 5 SYNONYM: HME, MATRIX METALLOPROTEINASE-12, MMP-12, MACROPHAGE COMPND 6 ELASTASE, ME; COMPND 7 EC: 3.4.24.65; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: MMP12, HME; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET21A KEYWDS MACROPHAGE ELASTASE, MATRIX METALLOPROTEINASE, PROTEIN-LIGAND KEYWDS 2 STRUCTURE, CATALYTIC DOMAIN, HUMAN GENE, CALCIUM, EXTRACELLULAR KEYWDS 3 MATRIX, GLYCOPROTEIN, HYDROLASE, METAL-BINDING, METALLOPROTEASE, KEYWDS 4 POLYMORPHISM, PROTEASE, SECRETED, ZINC, ZYMOGEN EXPDTA SOLUTION NMR NUMMDL 17 AUTHOR M.A.MARKUS,B.DWYER,S.WOLFROM,J.LI,W.LI,K.MALAKIAN,J.WILHELM, AUTHOR 2 D.H.H.TSAO REVDAT 4 16-MAR-22 2K2G 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2K2G 1 VERSN REVDAT 2 27-MAY-08 2K2G 1 JRNL REVDAT 1 20-MAY-08 2K2G 0 JRNL AUTH M.A.MARKUS,B.DWYER,S.WOLFROM,J.LI,W.LI,K.MALAKIAN,J.WILHELM, JRNL AUTH 2 D.H.TSAO JRNL TITL SOLUTION STRUCTURE OF WILD-TYPE HUMAN MATRIX JRNL TITL 2 METALLOPROTEINASE 12 (MMP-12) IN COMPLEX WITH A JRNL TITL 3 TIGHT-BINDING INHIBITOR. JRNL REF J.BIOMOL.NMR V. 41 55 2008 JRNL REFN ISSN 0925-2738 JRNL PMID 18425585 JRNL DOI 10.1007/S10858-008-9236-4 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.A.MARKUS,B.DWYER,S.WOLFROM,J.LI,W.LI,K.MALAKIAN,J.WILHELM, REMARK 1 AUTH 2 D.H.H.TSAO REMARK 1 TITL 1H, 13C, AND 15N ASSIGNMENTS OF MMP-12, A KEY PROTEASE REMARK 1 TITL 2 IMPLICATED IN LUNG TISSUE REMODELING REMARK 1 REF J.BIOMOL.NMR V. 31 260 2005 REMARK 1 REFN ISSN 0925-2738 REMARK 1 PMID 15803400 REMARK 1 DOI 10.1007/S10858-005-0181-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FOR STRUCTURES WITH NOE AND ANGLE REMARK 3 RESTRAINTS, TO INCORPORATE DIPOLAR COUPLINGS REMARK 4 REMARK 4 2K2G COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-APR-08. REMARK 100 THE DEPOSITION ID IS D_1000100591. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 160 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 700 UM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 700 UM DSV, 93% H2O/7% REMARK 210 D2O; 400 UM [U-100% 13C; U-100% REMARK 210 15N] PROTEIN, 400 UM DSV, 100% REMARK 210 D2O; 550 UM [U-10% 13C] PROTEIN, REMARK 210 550 UM DSV, 100% D2O; 400 UM [U- REMARK 210 100% 15N] PROTEIN, 400 UM DSV, REMARK 210 93% H2O/7% D2O; 400 UM [U-100% REMARK 210 15N] PROTEIN, 400 UM DSV, 93% REMARK 210 H2O/7% D2O; 250 UM [U-100% 13C; REMARK 210 U-100% 15N] PROTEIN, 250 UM DSV, REMARK 210 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNHA; 3D REMARK 210 HNHB; 3D HACACB; 3D LRCC; 3D 1H- REMARK 210 15N NOESY; 3D 13C-15N NOESY; 3D REMARK 210 1H-13C NOESY; 3D 13C-12C NOESY; REMARK 210 2D 1H-15N HSQC IPAP; 2D 1H-15N REMARK 210 HSQC NO C' DECOUPLING; 3D HNCO REMARK 210 NO CA DECOUPLING; 3D HACA(CO)NH REMARK 210 NO HA DECOUPLING REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : PIPP, X-PLOR NIH REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING, SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 17 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: CHEMICAL SHIFT ASSIGNMENTS WERE PREVIOUSLY REPORTED, SO REMARK 210 EXPERIMENTS TO SUPPORT THE ASSIGNMENTS WILL NOT BE DESCRIBED. 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: 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 HE2 HIS A 222 ZN ZN A 2 1.15 REMARK 500 HE2 HIS A 183 ZN ZN A 3 1.34 REMARK 500 O GLY A 193 H ALA A 195 1.38 REMARK 500 HE2 HIS A 168 ZN ZN A 3 1.41 REMARK 500 HG1 THR A 115 OD2 ASP A 158 1.43 REMARK 500 OG1 THR A 115 H ASP A 158 1.43 REMARK 500 O GLN A 259 H TYR A 262 1.51 REMARK 500 H THR A 115 OD2 ASP A 158 1.56 REMARK 500 HE2 HIS A 218 ZN ZN A 2 1.57 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 PHE A 100 14.53 -174.20 REMARK 500 1 MET A 103 66.10 -158.78 REMARK 500 1 VAL A 108 82.21 -54.37 REMARK 500 1 ARG A 110 33.40 -158.37 REMARK 500 1 LYS A 111 -10.87 61.80 REMARK 500 1 TYR A 121 -119.51 -133.30 REMARK 500 1 ASP A 124 -22.78 -168.83 REMARK 500 1 PRO A 146 33.54 -77.60 REMARK 500 1 HIS A 168 51.24 -160.84 REMARK 500 1 ASP A 170 158.46 -45.38 REMARK 500 1 PHE A 171 165.86 54.49 REMARK 500 1 HIS A 172 26.57 -74.96 REMARK 500 1 ALA A 173 141.66 66.55 REMARK 500 1 ASP A 194 54.55 -60.38 REMARK 500 1 ASP A 200 -17.45 -44.49 REMARK 500 1 THR A 204 116.91 -160.29 REMARK 500 1 SER A 207 -129.67 84.88 REMARK 500 1 LEU A 224 39.59 -82.98 REMARK 500 1 ASP A 231 55.36 -175.49 REMARK 500 1 PRO A 232 43.93 -86.52 REMARK 500 1 LYS A 233 45.78 39.24 REMARK 500 1 VAL A 235 -10.86 -48.76 REMARK 500 1 PHE A 237 141.48 -39.41 REMARK 500 1 ASP A 244 -178.51 -52.89 REMARK 500 2 PHE A 100 9.64 -172.66 REMARK 500 2 MET A 103 63.97 -161.56 REMARK 500 2 PRO A 104 101.98 -42.17 REMARK 500 2 VAL A 108 -48.99 -150.70 REMARK 500 2 TYR A 121 -151.80 35.61 REMARK 500 2 THR A 122 115.70 -174.50 REMARK 500 2 ASN A 126 108.27 -51.32 REMARK 500 2 PRO A 146 31.52 -78.55 REMARK 500 2 PHE A 171 26.00 46.11 REMARK 500 2 ALA A 173 141.96 -174.61 REMARK 500 2 PRO A 187 34.11 -70.39 REMARK 500 2 ILE A 191 -5.08 -51.50 REMARK 500 2 ASP A 194 83.75 -19.32 REMARK 500 2 ASP A 200 -17.44 -42.50 REMARK 500 2 THR A 204 109.55 -160.18 REMARK 500 2 HIS A 206 -5.37 -150.29 REMARK 500 2 SER A 207 99.18 87.16 REMARK 500 2 LEU A 224 36.61 -79.24 REMARK 500 2 SER A 229 -145.14 -117.01 REMARK 500 2 ASP A 231 59.75 171.43 REMARK 500 2 PRO A 238 -121.13 -38.78 REMARK 500 2 TYR A 242 105.66 -49.90 REMARK 500 2 ASP A 244 -178.47 -56.34 REMARK 500 2 GLN A 259 -15.47 -44.38 REMARK 500 2 SER A 260 -11.42 -48.69 REMARK 500 3 ARG A 101 -16.87 -161.45 REMARK 500 REMARK 500 THIS ENTRY HAS 470 RAMACHANDRAN OUTLIERS. 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 ZN A 2 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DSV A 1 O40 REMARK 620 2 HIS A 218 NE2 93.0 REMARK 620 3 HIS A 222 NE2 84.7 96.9 REMARK 620 4 HIS A 228 NE2 89.8 156.7 106.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 3 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 168 NE2 REMARK 620 2 HIS A 183 NE2 147.7 REMARK 620 3 HIS A 196 ND1 112.3 98.7 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 3 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSV A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6391 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENTS DBREF 2K2G A 100 263 UNP P39900 MMP12_HUMAN 100 263 SEQADV 2K2G MET A 99 UNP P39900 INITIATING METHIONINE SEQRES 1 A 165 MET PHE ARG GLU MET PRO GLY GLY PRO VAL TRP ARG LYS SEQRES 2 A 165 HIS TYR ILE THR TYR ARG ILE ASN ASN TYR THR PRO ASP SEQRES 3 A 165 MET ASN ARG GLU ASP VAL ASP TYR ALA ILE ARG LYS ALA SEQRES 4 A 165 PHE GLN VAL TRP SER ASN VAL THR PRO LEU LYS PHE SER SEQRES 5 A 165 LYS ILE ASN THR GLY MET ALA ASP ILE LEU VAL VAL PHE SEQRES 6 A 165 ALA ARG GLY ALA HIS GLY ASP PHE HIS ALA PHE ASP GLY SEQRES 7 A 165 LYS GLY GLY ILE LEU ALA HIS ALA PHE GLY PRO GLY SER SEQRES 8 A 165 GLY ILE GLY GLY ASP ALA HIS PHE ASP GLU ASP GLU PHE SEQRES 9 A 165 TRP THR THR HIS SER GLY GLY THR ASN LEU PHE LEU THR SEQRES 10 A 165 ALA VAL HIS GLU ILE GLY HIS SER LEU GLY LEU GLY HIS SEQRES 11 A 165 SER SER ASP PRO LYS ALA VAL MET PHE PRO THR TYR LYS SEQRES 12 A 165 TYR VAL ASP ILE ASN THR PHE ARG LEU SER ALA ASP ASP SEQRES 13 A 165 ILE ARG GLY ILE GLN SER LEU TYR GLY HET ZN A 2 1 HET ZN A 3 1 HET DSV A 1 40 HETNAM ZN ZINC ION HETNAM DSV N-(DIBENZO[B,D]THIOPHEN-3-YLSULFONYL)-L-VALINE FORMUL 2 ZN 2(ZN 2+) FORMUL 4 DSV C17 H17 N O4 S2 HELIX 1 1 ASN A 126 VAL A 144 1 19 HELIX 2 2 SER A 189 GLY A 193 5 5 HELIX 3 3 ASN A 211 LEU A 224 1 14 HELIX 4 4 SER A 251 GLN A 259 1 9 HELIX 5 5 SER A 260 TYR A 262 5 3 SHEET 1 A 3 TYR A 116 ILE A 118 0 SHEET 2 A 3 ILE A 159 ALA A 164 1 O VAL A 161 N ARG A 117 SHEET 3 A 3 HIS A 196 ASP A 198 1 O PHE A 197 N VAL A 162 LINK O40 DSV A 1 ZN ZN A 2 1555 1555 2.36 LINK ZN ZN A 2 NE2 HIS A 218 1555 1555 2.22 LINK ZN ZN A 2 NE2 HIS A 222 1555 1555 2.01 LINK ZN ZN A 2 NE2 HIS A 228 1555 1555 2.30 LINK ZN ZN A 3 NE2 HIS A 168 1555 1555 2.25 LINK ZN ZN A 3 NE2 HIS A 183 1555 1555 2.15 LINK ZN ZN A 3 ND1 HIS A 196 1555 1555 2.17 SITE 1 AC1 2 HIS A 218 HIS A 222 SITE 1 AC2 2 HIS A 168 PHE A 171 SITE 1 AC3 12 GLY A 179 ILE A 180 LEU A 181 HIS A 183 SITE 2 AC3 12 ALA A 184 ASN A 211 LEU A 214 THR A 215 SITE 3 AC3 12 HIS A 218 HIS A 222 HIS A 228 MET A 236 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