1CME - Header Asymmetric Unit

HEADER OXIDOREDUCTASE(NAD(A)-CHOH(D)) 21-MAR-92 1CME

TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI MALATE DEHYDROGENASE. TITLE 2 A COMPLEX OF THE APOENZYME AND CITRATE AT 1.87 ANGSTROMS TITLE 3 RESOLUTION

COMPND MOL_ID: 1; COMPND 2 MOLECULE: MALATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.1.1.37; COMPND 5 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI

KEYWDS OXIDOREDUCTASE(NAD(A)-CHOH(D))

EXPDTA THEORETICAL MODEL

AUTHOR M.D.HALL,L.J.BANASZAK

REVDAT 2 01-APR-03 1CME 1 JRNL REVDAT 1 31-JAN-94 1CME 0

JRNL AUTH M.D.HALL,D.G.LEVITT,L.J.BANASZAK JRNL TITL CRYSTAL STRUCTURE OF ESCHERICHIA COLI MALATE JRNL TITL 2 DEHYDROGENASE. A COMPLEX OF THE APOENZYME AND JRNL TITL 3 CITRATE AT 1.87 A RESOLUTION. JRNL REF J.MOL.BIOL. V. 226 867 1992 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 1CME COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998

REMARK 5 REMARK 5 THIS STRUCTURE REPRESENTS A MODEL OF A TERNARY COMPLEX IN REMARK 5 WHICH AN NAD MOLECULE FROM THE CRYSTAL STRUCTURE OF REMARK 5 PORCINE CYTOPLASMIC MALATE DEHYDROGENASE (4MDH) WAS PLACED REMARK 5 INTO THE NAD BINDING SITE OF EMDH AND THE CITRATE ION IN REMARK 5 THE ACTIVE SITE OF EMDH WAS TRIMMED TO FORM A MALATE REMARK 5 MOLECULE AFTER WHICH THE ENTIRE TERNARY COMPLEX WAS ENERGY REMARK 5 MINIMIZED WITH X-PLOR. THIS IS, THEREFORE, NOT A CRYSTAL REMARK 5 STRUCTURE BUT IS BASED ON THE EMDH AND 4MDH STRUCTURES AND REMARK 5 REPRESENTS A HYPOTHETICAL STRUCTURE. SINCE THIS IS AN REMARK 5 ENERGY MINIMIZED STRUCTURE AND NOT A REFINED ONE, THERE REMARK 5 WAS NO WEIGHTING FOR X-RAY DATA. CONSEQUENTLY THE GEOMETRY REMARK 5 TERMS WERE COMPLETELY FAVORED IN THE PROCESS.

REMARK 6 REMARK 6 SEQUENCE ADVISORY NOTICE: REMARK 6 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 6 REMARK 6 SWISS-PROT ENTRY NAME: MDH_ECOLI REMARK 6 REMARK 6 SWISS-PROT RESIDUE PDB SEQRES REMARK 6 NAME NUMBER NAME CHAIN SEQ/INSERT CODE REMARK 6 GLN 259 ASN 259 REMARK 6 REMARK 6 THE DEPOSITORS BELIEVE THAT THE SWISS-PROT ENTRY IS REMARK 6 INCORRECT.

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL

REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.

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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 HIS A 48 NE2 HIS A 48 CD2 -0.071 REMARK 500 VAL A 171 CA VAL A 171 CB 0.072 REMARK 500 HIS A 177 NE2 HIS A 177 CD2 -0.069

DBREF 1CME A 1 312 UNP P06994 MDH_ECOLI 1 312

SEQADV 1CME ARG A 80 UNP P06994 ALA 80 CONFLICT SEQADV 1CME ASN A 259 UNP P06994 GLN 259 CONFLICT SEQADV 1CME GLN A 307 UNP P06994 GLU 307 CONFLICT

SEQRES 1 A 312 MET LYS VAL ALA VAL LEU GLY ALA ALA GLY GLY ILE GLY SEQRES 2 A 312 GLN ALA LEU ALA LEU LEU LEU LYS THR GLN LEU PRO SER SEQRES 3 A 312 GLY SER GLU LEU SER LEU TYR ASP ILE ALA PRO VAL THR SEQRES 4 A 312 PRO GLY VAL ALA VAL ASP LEU SER HIS ILE PRO THR ALA SEQRES 5 A 312 VAL LYS ILE LYS GLY PHE SER GLY GLU ASP ALA THR PRO SEQRES 6 A 312 ALA LEU GLU GLY ALA ASP VAL VAL LEU ILE SER ALA GLY SEQRES 7 A 312 VAL ARG ARG LYS PRO GLY MET ASP ARG SER ASP LEU PHE SEQRES 8 A 312 ASN VAL ASN ALA GLY ILE VAL LYS ASN LEU VAL GLN GLN SEQRES 9 A 312 VAL ALA LYS THR CYS PRO LYS ALA CYS ILE GLY ILE ILE SEQRES 10 A 312 THR ASN PRO VAL ASN THR THR VAL ALA ILE ALA ALA GLU SEQRES 11 A 312 VAL LEU LYS LYS ALA GLY VAL TYR ASP LYS ASN LYS LEU SEQRES 12 A 312 PHE GLY VAL THR THR LEU ASP ILE ILE ARG SER ASN THR SEQRES 13 A 312 PHE VAL ALA GLU LEU LYS GLY LYS GLN PRO GLY GLU VAL SEQRES 14 A 312 GLU VAL PRO VAL ILE GLY GLY HIS SER GLY VAL THR ILE SEQRES 15 A 312 LEU PRO LEU LEU SER GLN VAL PRO GLY VAL SER PHE THR SEQRES 16 A 312 GLU GLN GLU VAL ALA ASP LEU THR LYS ARG ILE GLN ASN SEQRES 17 A 312 ALA GLY THR GLU VAL VAL GLU ALA LYS ALA GLY GLY GLY SEQRES 18 A 312 SER ALA THR LEU SER MET GLY GLN ALA ALA ALA ARG PHE SEQRES 19 A 312 GLY LEU SER LEU VAL ARG ALA LEU GLN GLY GLU GLN GLY SEQRES 20 A 312 VAL VAL GLU CYS ALA TYR VAL GLU GLY ASP GLY ASN TYR SEQRES 21 A 312 ALA ARG PHE PHE SER GLN PRO LEU LEU LEU GLY LYS ASN SEQRES 22 A 312 GLY VAL GLU GLU ARG LYS SER ILE GLY THR LEU SER ALA SEQRES 23 A 312 PHE GLU GLN ASN ALA LEU GLU GLY MET LEU ASP THR LEU SEQRES 24 A 312 LYS LYS ASP ILE ALA LEU GLY GLN GLU PHE VAL ASN LYS

FTNOTE 1 RESIDUE PRO 120 IS A CIS PROLINE.

HET MLT 313 9 HET NAD 314 44

HETNAM MLT MALATE ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE

FORMUL 2 MLT C4 H5 O5 1- FORMUL 3 NAD C21 H27 N7 O14 P2 FORMUL 4 HOH *88(H2 O1)

HELIX 1 B GLY A 10 GLN A 23 1 14 HELIX 2 C ALA A 36 ILE A 49 1 14 HELIX 3 C' ALA A 63 GLU A 68 1 6 HELIX 4 DE ASP A 86 THR A 108 1 23 HELIX 5 1F ASN A 119 LEU A 132 1 14 HELIX 6 2F GLY A 145 GLU A 160 1 16 HELIX 7 1GG VAL A 192 VAL A 213 1 22 HELIX 8 3G GLY A 221 ARG A 240 1 20 HELIX 9 H SER A 285 LYS A 312 1 28

SHEET 1 S1 6 MET A 1 GLY A 7 0 SHEET 2 S1 6 GLY A 27 ASP A 34 1 SHEET 3 S1 6 VAL A 53 SER A 59 1 SHEET 4 S1 6 ASP A 71 LEU A 74 -1 SHEET 5 S1 6 CYS A 113 ILE A 116 -1 SHEET 6 S1 6 ASN A 141 GLY A 145 -1 SHEET 1 S2 2 GLU A 170 ILE A 174 0 SHEET 2 S2 2 GLY A 179 LEU A 185 -1 SHEET 1 S3 3 GLU A 245 TYR A 253 0 SHEET 2 S3 3 ALA A 261 PRO A 267 -1 SHEET 3 S3 3 LEU A 270 GLY A 274 -1

TURN 1 T01 GLY A 10 GLY A 13 TURN 2 T02 PRO A 25 SER A 28 TURN 3 T03 ALA A 36 THR A 39 TURN 4 T04 SER A 59 ASP A 62 TURN 5 T05 LYS A 82 MET A 85 TURN 6 T06 CYS A 109 ALA A 112 TURN 7 T07 THR A 118 VAL A 121 TURN 8 T08 GLN A 165 GLU A 168 TURN 9 T09 VAL A 189 VAL A 192 TURN 10 T10 LYS A 217 GLY A 220 TURN 11 T12 GLY A 271 GLY A 274

CISPEP 1 ASN A 119 PRO A 120 0 -22.16

SITE 1 ACT 5 ARG A 81 ARG A 87 ASP A 150 ARG A 153 SITE 2 ACT 5 HIS A 177

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