HEADER OXIDOREDUCTASE 27-AUG-20 7JXG TITLE STRUCTURAL MODEL FOR FE-CONTAINING HUMAN ACIREDUCTONE DIOXYGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1,2-DIHYDROXY-3-KETO-5-METHYLTHIOPENTENE DIOXYGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ACIREDUCTONE DIOXYGENASE (FE(2+)-REQUIRING),FE-ARD,MEMBRANE- COMPND 5 TYPE 1 MATRIX METALLOPROTEINASE CYTOPLASMIC TAIL-BINDING PROTEIN 1, COMPND 6 MTCBP-1,SUBMERGENCE-INDUCED PROTEIN-LIKE FACTOR,SIP-L; COMPND 7 EC: 1.13.11.54; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ADI1, MTCBP1, HMFT1638; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CUPIN BARREL, METHIONINE SALVAGE, CANCER, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 6 AUTHOR T.C.POCHAPSKY,X.LIU,A.DESHPANDE,D.RINGE,A.GARBER,J.RYAN REVDAT 3 01-MAY-24 7JXG 1 REMARK REVDAT 2 25-NOV-20 7JXG 1 JRNL REVDAT 1 18-NOV-20 7JXG 0 JRNL AUTH X.LIU,A.GARBER,J.RYAN,A.DESHPANDE,D.RINGE,T.C.POCHAPSKY JRNL TITL A MODEL FOR THE SOLUTION STRUCTURE OF HUMAN FE(II)-BOUND JRNL TITL 2 ACIREDUCTONE DIOXYGENASE AND INTERACTIONS WITH THE JRNL TITL 3 REGULATORY DOMAIN OF MATRIX METALLOPROTEINASE I (MMP-I). JRNL REF BIOCHEMISTRY V. 59 4238 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 33135413 JRNL DOI 10.1021/ACS.BIOCHEM.0C00724 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH 2.51 REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7JXG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000250757. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298 REMARK 210 PH : 7.4; 7.4 REMARK 210 IONIC STRENGTH : 0.1; 0.1 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 400 UM [U-100% 13C; U-100% 15N] REMARK 210 HUMAN FE(II)-BOUND ACIREDUCTONE REMARK 210 DIOXYGENASE, 95% H2O/5% D2O; 400 REMARK 210 UM [U-15N] HUMAN FE(II)-BOUND REMARK 210 ACIREDUCTONE DIOXYGENASE, 10 MG/ REMARK 210 ML BACTERIOPHAGE PF1, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H,15N TROSY-HSQC; 1H,13C HSQC; REMARK 210 HNCA; HN(CO)CA; HNCACB; 15N- REMARK 210 SEPARATED NOESY; 1H,1H NOESY; REMARK 210 HCCH-TOCSY; 13C-SEPARATED NOESY; REMARK 210 IPAP 15N-SEPARATED TROSY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : NEO REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRFAM-SPARKY 1.4 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 6 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: 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 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 MODELS 1-6 REMARK 465 RES C SSSEQI REMARK 465 ALA A 179 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 O LEU A 41 OH TYR A 97 2.17 REMARK 500 O LYS A 173 OE1 GLN A 177 2.19 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 50 -8.43 -46.40 REMARK 500 1 PRO A 75 154.14 -49.97 REMARK 500 1 ASN A 76 32.54 70.18 REMARK 500 1 VAL A 137 25.91 -165.05 REMARK 500 1 TYR A 142 96.38 -173.15 REMARK 500 1 PRO A 153 96.02 -55.46 REMARK 500 1 ARG A 160 -74.00 -43.26 REMARK 500 2 PRO A 50 -8.95 -42.95 REMARK 500 2 CYS A 70 113.63 -170.11 REMARK 500 2 ASN A 76 22.13 86.10 REMARK 500 2 ASP A 100 -31.79 -146.80 REMARK 500 2 VAL A 137 18.80 -165.55 REMARK 500 2 ASN A 141 11.92 47.48 REMARK 500 3 TYR A 6 68.58 -104.42 REMARK 500 3 PRO A 17 2.29 -59.50 REMARK 500 3 PRO A 50 -8.05 -41.05 REMARK 500 3 CYS A 70 128.27 -171.12 REMARK 500 3 PRO A 75 176.40 -41.01 REMARK 500 3 ASP A 100 -21.08 -144.88 REMARK 500 3 GLU A 111 -9.14 -59.81 REMARK 500 3 ASN A 141 -10.99 68.32 REMARK 500 4 PRO A 50 -8.69 -49.47 REMARK 500 4 CYS A 70 110.18 -172.06 REMARK 500 4 PRO A 75 172.93 -40.74 REMARK 500 4 HIS A 90 146.48 -170.71 REMARK 500 4 ASP A 112 32.09 76.62 REMARK 500 4 LYS A 140 4.28 -159.95 REMARK 500 4 PRO A 153 95.25 -69.51 REMARK 500 5 TYR A 6 77.29 -108.71 REMARK 500 5 HIS A 18 39.03 71.71 REMARK 500 5 PRO A 50 -9.30 -44.06 REMARK 500 5 CYS A 70 118.52 -164.63 REMARK 500 5 ASN A 76 38.03 70.86 REMARK 500 5 HIS A 90 140.71 -170.70 REMARK 500 5 ASP A 112 40.61 76.17 REMARK 500 5 LYS A 140 -22.89 -140.66 REMARK 500 5 PRO A 153 71.25 -57.53 REMARK 500 6 PRO A 50 -8.52 -48.70 REMARK 500 6 ASN A 76 39.13 74.65 REMARK 500 6 LEU A 91 16.85 -67.78 REMARK 500 6 GLU A 111 2.89 -63.77 REMARK 500 6 ASP A 112 41.54 76.51 REMARK 500 6 VAL A 137 17.44 -164.96 REMARK 500 6 TYR A 142 96.63 -172.94 REMARK 500 6 PRO A 153 78.80 -65.02 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 FE2 A 201 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 88 NE2 REMARK 620 2 HIS A 90 NE2 90.2 REMARK 620 3 GLU A 94 OE1 179.2 90.2 REMARK 620 4 HIS A 133 NE2 90.6 89.4 90.1 REMARK 620 5 HOH A 301 O 89.6 90.2 89.7 179.5 REMARK 620 6 HOH A 302 O 89.8 179.6 89.8 90.2 90.2 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 50269 RELATED DB: BMRB DBREF 7JXG A 1 179 UNP Q9BV57 MTND_HUMAN 1 179 SEQRES 1 A 179 MET VAL GLN ALA TRP TYR MET ASP ASP ALA PRO GLY ASP SEQRES 2 A 179 PRO ARG GLN PRO HIS ARG PRO ASP PRO GLY ARG PRO VAL SEQRES 3 A 179 GLY LEU GLU GLN LEU ARG ARG LEU GLY VAL LEU TYR TRP SEQRES 4 A 179 LYS LEU ASP ALA ASP LYS TYR GLU ASN ASP PRO GLU LEU SEQRES 5 A 179 GLU LYS ILE ARG ARG GLU ARG ASN TYR SER TRP MET ASP SEQRES 6 A 179 ILE ILE THR ILE CYS LYS ASP LYS LEU PRO ASN TYR GLU SEQRES 7 A 179 GLU LYS ILE LYS MET PHE TYR GLU GLU HIS LEU HIS LEU SEQRES 8 A 179 ASP ASP GLU ILE ARG TYR ILE LEU ASP GLY SER GLY TYR SEQRES 9 A 179 PHE ASP VAL ARG ASP LYS GLU ASP GLN TRP ILE ARG ILE SEQRES 10 A 179 PHE MET GLU LYS GLY ASP MET VAL THR LEU PRO ALA GLY SEQRES 11 A 179 ILE TYR HIS ARG PHE THR VAL ASP GLU LYS ASN TYR THR SEQRES 12 A 179 LYS ALA MET ARG LEU PHE VAL GLY GLU PRO VAL TRP THR SEQRES 13 A 179 ALA TYR ASN ARG PRO ALA ASP HIS PHE GLU ALA ARG GLY SEQRES 14 A 179 GLN TYR VAL LYS PHE LEU ALA GLN THR ALA HET FE2 A 201 1 HETNAM FE2 FE (II) ION FORMUL 2 FE2 FE 2+ FORMUL 3 HOH *2(H2 O) HELIX 1 AA1 TYR A 6 ALA A 10 5 5 HELIX 2 AA2 GLY A 27 GLY A 35 1 9 HELIX 3 AA3 ASP A 42 ASN A 48 1 7 HELIX 4 AA4 PRO A 50 ARG A 59 1 10 HELIX 5 AA5 ASN A 76 GLU A 86 1 11 HELIX 6 AA6 VAL A 154 TYR A 158 5 5 HELIX 7 AA7 PRO A 161 HIS A 164 5 4 HELIX 8 AA8 PHE A 165 THR A 178 1 14 SHEET 1 AA1 4 GLN A 3 TRP A 5 0 SHEET 2 AA1 4 GLN A 113 MET A 119 -1 O PHE A 118 N GLN A 3 SHEET 3 AA1 4 GLY A 103 ASP A 109 -1 N GLY A 103 O MET A 119 SHEET 4 AA1 4 HIS A 133 THR A 136 -1 O ARG A 134 N ASP A 106 SHEET 1 AA2 4 TRP A 63 ILE A 69 0 SHEET 2 AA2 4 THR A 143 PHE A 149 -1 O THR A 143 N ILE A 69 SHEET 3 AA2 4 GLU A 94 GLY A 101 -1 N ASP A 100 O LYS A 144 SHEET 4 AA2 4 MET A 124 LEU A 127 -1 O VAL A 125 N ARG A 96 LINK NE2 HIS A 88 FE FE2 A 201 1555 1555 2.09 LINK NE2 HIS A 90 FE FE2 A 201 1555 1555 2.09 LINK OE1 GLU A 94 FE FE2 A 201 1555 1555 2.09 LINK NE2 HIS A 133 FE FE2 A 201 1555 1555 2.09 LINK FE FE2 A 201 O HOH A 301 1555 1555 1.90 LINK FE FE2 A 201 O HOH A 302 1555 1555 1.90 CISPEP 1 ASP A 21 PRO A 22 1 -0.32 CISPEP 2 ASP A 21 PRO A 22 2 -1.15 CISPEP 3 ASP A 21 PRO A 22 3 -0.52 CISPEP 4 ASP A 21 PRO A 22 4 -0.35 CISPEP 5 ASP A 21 PRO A 22 5 -0.61 CISPEP 6 ASP A 21 PRO A 22 6 -0.11 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