HEADER HYDROLASE 30-JAN-09 2KEM TITLE EXTENDED STRUCTURE OF CITIDINE DEAMINASE DOMAIN OF APOBEC3G COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA DC->DU-EDITING ENZYME APOBEC-3G; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 191-284; COMPND 5 SYNONYM: APOBEC-RELATED CYTIDINE DEAMINASE, ARCD, APOBEC-RELATED COMPND 6 PROTEIN, ARP-9, CEM-15, CEM15; COMPND 7 EC: 3.5.4.-; COMPND 8 ENGINEERED: YES; COMPND 9 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: APOBEC3G; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-DE3(RIL); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PGEX6P1 KEYWDS HELIX, SHEET, ZINC, ALTERNATIVE SPLICING, ANTIVIRAL DEFENSE, KEYWDS 2 CYTOPLASM, HOST-VIRUS INTERACTION, HYDROLASE, METAL-BINDING, KEYWDS 3 NUCLEUS, POLYMORPHISM, UBL CONJUGATION EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR E.HARJES,P.J.GROSS,K.CHEN,Y.LU,K.SHINDO,R.NOWARSKI,J.D.GROSS, AUTHOR 2 M.KOTLER,R.S.HARRIS,H.MATSUO REVDAT 4 29-MAY-24 2KEM 1 REMARK REVDAT 3 10-NOV-21 2KEM 1 REMARK SEQADV REVDAT 2 07-JUL-09 2KEM 1 JRNL REVDAT 1 02-JUN-09 2KEM 0 JRNL AUTH E.HARJES,P.J.GROSS,K.M.CHEN,Y.LU,K.SHINDO,R.NOWARSKI, JRNL AUTH 2 J.D.GROSS,M.KOTLER,R.S.HARRIS,H.MATSUO JRNL TITL AN EXTENDED STRUCTURE OF THE APOBEC3G CATALYTIC DOMAIN JRNL TITL 2 SUGGESTS A UNIQUE HOLOENZYME MODEL JRNL REF J.MOL.BIOL. V. 389 819 2009 JRNL REFN ISSN 0022-2836 JRNL PMID 19389408 JRNL DOI 10.1016/J.JMB.2009.04.031 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: CNS REMARK 4 REMARK 4 2KEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-FEB-09. REMARK 100 THE DEPOSITION ID IS D_1000101025. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-100% 15N] APOBEC3G-1, REMARK 210 90% H2O/10% D2O; 0.3 MM [U-13C; REMARK 210 U-15N; U-2H] APOBEC3G-2, 90% H2O/ REMARK 210 10% D2O; 0.3 MM [U-15N; U-50% 2H] REMARK 210 APOBEC3G-3, 90% H2O/10% D2O; REMARK 210 0.3 MM [U-100% 13C] APOBEC3G-4, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCACB; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ; 800 MHZ; 900 MHZ; 600 REMARK 210 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A -7 REMARK 465 PRO A -6 REMARK 465 LEU A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 PHE A 0 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 ALA A 106 H LYS A 111 1.52 REMARK 500 O VAL A 75 H TRP A 79 1.58 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 ILE A 2 -113.02 -132.68 REMARK 500 1 SER A 6 135.00 164.41 REMARK 500 1 MET A 7 -147.04 -79.64 REMARK 500 1 THR A 11 -65.31 -97.22 REMARK 500 1 TRP A 21 142.06 63.01 REMARK 500 1 ARG A 25 96.07 -44.58 REMARK 500 1 HIS A 26 149.83 -177.49 REMARK 500 1 HIS A 38 68.00 -108.91 REMARK 500 1 ASP A 40 -23.66 129.37 REMARK 500 1 TRP A 42 86.71 -155.28 REMARK 500 1 LEU A 45 -166.63 -61.38 REMARK 500 1 ARG A 48 117.25 177.51 REMARK 500 1 ALA A 53 83.14 -155.71 REMARK 500 1 HIS A 58 -165.38 -177.83 REMARK 500 1 LYS A 59 44.10 -144.53 REMARK 500 1 HIS A 60 -175.20 -177.97 REMARK 500 1 LEU A 63 94.54 -54.52 REMARK 500 1 ALA A 68 -35.99 -38.16 REMARK 500 1 ASP A 82 -63.85 79.64 REMARK 500 1 PRO A 97 -72.29 -94.98 REMARK 500 1 CYS A 98 149.86 153.62 REMARK 500 1 ASN A 112 -66.79 -101.58 REMARK 500 1 LYS A 113 115.73 66.34 REMARK 500 1 HIS A 114 28.26 -177.02 REMARK 500 1 TYR A 125 106.53 -49.61 REMARK 500 1 GLN A 128 37.29 -149.35 REMARK 500 1 ALA A 131 -48.18 80.47 REMARK 500 1 ALA A 141 -27.64 -172.25 REMARK 500 1 ALA A 143 113.46 176.55 REMARK 500 1 LYS A 144 94.37 -67.31 REMARK 500 1 THR A 149 -169.57 -108.09 REMARK 500 1 HIS A 163 -40.33 158.65 REMARK 500 1 GLN A 164 27.54 49.63 REMARK 500 1 PRO A 167 -70.94 -58.88 REMARK 500 1 TRP A 171 -66.76 69.57 REMARK 500 1 ASP A 172 -62.08 81.88 REMARK 500 2 ILE A 2 -160.72 -100.64 REMARK 500 2 SER A 6 124.62 165.40 REMARK 500 2 MET A 7 -150.02 -79.41 REMARK 500 2 THR A 11 -65.22 -95.54 REMARK 500 2 ARG A 23 -75.58 -47.20 REMARK 500 2 ARG A 25 79.63 42.98 REMARK 500 2 GLU A 27 48.12 -81.51 REMARK 500 2 THR A 28 108.13 9.33 REMARK 500 2 HIS A 38 67.21 -113.48 REMARK 500 2 ASP A 40 -23.02 129.24 REMARK 500 2 TRP A 42 87.03 -155.19 REMARK 500 2 ARG A 48 -84.84 -81.66 REMARK 500 2 ARG A 49 46.82 78.84 REMARK 500 2 ALA A 53 91.62 -162.18 REMARK 500 REMARK 500 THIS ENTRY HAS 384 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 195 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 67 ND1 REMARK 620 2 CYS A 98 SG 115.5 REMARK 620 3 CYS A 101 SG 112.8 78.0 REMARK 620 N 1 2 REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR DETERMINED REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: AUTHOR DETERMINED 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 195 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2JYW RELATED DB: PDB REMARK 900 198-384 APOBEC3G NMR REMARK 900 RELATED ID: 3E1U RELATED DB: PDB REMARK 900 197-384 APOBEC3G CRYSTAL REMARK 900 RELATED ID: 2KBO RELATED DB: PDB REMARK 900 193-384 APOBEC3G NMR DBREF 2KEM A 1 194 UNP Q9HC16 ABC3G_HUMAN 191 384 SEQADV 2KEM GLY A -7 UNP Q9HC16 EXPRESSION TAG SEQADV 2KEM PRO A -6 UNP Q9HC16 EXPRESSION TAG SEQADV 2KEM LEU A -5 UNP Q9HC16 EXPRESSION TAG SEQADV 2KEM GLY A -4 UNP Q9HC16 EXPRESSION TAG SEQADV 2KEM SER A -3 UNP Q9HC16 EXPRESSION TAG SEQADV 2KEM PRO A -2 UNP Q9HC16 EXPRESSION TAG SEQADV 2KEM GLY A -1 UNP Q9HC16 EXPRESSION TAG SEQADV 2KEM PHE A 0 UNP Q9HC16 EXPRESSION TAG SEQADV 2KEM LYS A 44 UNP Q9HC16 LEU 234 ENGINEERED MUTATION SEQADV 2KEM ALA A 53 UNP Q9HC16 CYS 243 ENGINEERED MUTATION SEQADV 2KEM LYS A 120 UNP Q9HC16 PHE 310 ENGINEERED MUTATION SEQADV 2KEM ALA A 131 UNP Q9HC16 CYS 321 ENGINEERED MUTATION SEQADV 2KEM ALA A 166 UNP Q9HC16 CYS 356 ENGINEERED MUTATION SEQRES 1 A 202 GLY PRO LEU GLY SER PRO GLY PHE GLU ILE LEU ARG HIS SEQRES 2 A 202 SER MET ASP PRO PRO THR PHE THR PHE ASN PHE ASN ASN SEQRES 3 A 202 GLU PRO TRP VAL ARG GLY ARG HIS GLU THR TYR LEU CYS SEQRES 4 A 202 TYR GLU VAL GLU ARG MET HIS ASN ASP THR TRP VAL LYS SEQRES 5 A 202 LEU ASN GLN ARG ARG GLY PHE LEU ALA ASN GLN ALA PRO SEQRES 6 A 202 HIS LYS HIS GLY PHE LEU GLU GLY ARG HIS ALA GLU LEU SEQRES 7 A 202 CYS PHE LEU ASP VAL ILE PRO PHE TRP LYS LEU ASP LEU SEQRES 8 A 202 ASP GLN ASP TYR ARG VAL THR CYS PHE THR SER TRP SER SEQRES 9 A 202 PRO CYS PHE SER CYS ALA GLN GLU MET ALA LYS PHE ILE SEQRES 10 A 202 SER LYS ASN LYS HIS VAL SER LEU CYS ILE LYS THR ALA SEQRES 11 A 202 ARG ILE TYR ASP ASP GLN GLY ARG ALA GLN GLU GLY LEU SEQRES 12 A 202 ARG THR LEU ALA GLU ALA GLY ALA LYS ILE SER ILE MET SEQRES 13 A 202 THR TYR SER GLU PHE LYS HIS CYS TRP ASP THR PHE VAL SEQRES 14 A 202 ASP HIS GLN GLY ALA PRO PHE GLN PRO TRP ASP GLY LEU SEQRES 15 A 202 ASP GLU HIS SER GLN ASP LEU SER GLY ARG LEU ARG ALA SEQRES 16 A 202 ILE LEU GLN ASN GLN GLU ASN HET ZN A 195 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 THR A 11 PHE A 16 1 6 HELIX 2 2 HIS A 67 TRP A 79 1 13 HELIX 3 3 CYS A 98 SER A 110 1 13 HELIX 4 4 ARG A 130 ALA A 141 1 12 HELIX 5 5 THR A 149 PHE A 160 1 12 HELIX 6 7 ASP A 172 LEU A 189 1 18 SHEET 1 A 5 THR A 41 VAL A 43 0 SHEET 2 A 5 LEU A 30 HIS A 38 -1 N HIS A 38 O THR A 41 SHEET 3 A 5 ASP A 86 PHE A 92 -1 O THR A 90 N GLU A 33 SHEET 4 A 5 VAL A 115 THR A 121 1 SHEET 5 A 5 LYS A 144 ILE A 147 1 O LYS A 144 N LEU A 117 SHEET 1 B 5 GLY A 50 LEU A 52 0 SHEET 2 B 5 LEU A 30 HIS A 38 -1 N HIS A 38 O THR A 41 SHEET 3 B 5 ASP A 86 PHE A 92 -1 O THR A 90 N GLU A 33 SHEET 4 B 5 VAL A 115 THR A 121 1 SHEET 5 B 5 LYS A 144 ILE A 147 1 O LYS A 144 N LEU A 117 LINK ND1 HIS A 67 ZN ZN A 195 1555 1555 2.26 LINK SG CYS A 98 ZN ZN A 195 1555 1555 2.30 LINK SG CYS A 101 ZN ZN A 195 1555 1555 2.31 SITE 1 AC1 5 HIS A 67 GLU A 69 PRO A 97 CYS A 98 SITE 2 AC1 5 CYS A 101 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