HEADER OXIDOREDUCTASE 17-FEB-12 4AJR
TITLE 3D STRUCTURE OF E. COLI ISOCITRATE DEHYDROGENASE K100M MUTANT IN
TITLE 2 COMPLEX WITH ALPHA-KETOGLUTARATE, MAGNESIUM(II) AND NADPH - THE
TITLE 3 PRODUCT COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ISOCITRATE DEHYDROGENASE [NADP];
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: IDH, IDP, NADP(+)-SPECIFIC ICDH, OXALOSUCCINATE
COMPND 5 DECARBOXYLASE;
COMPND 6 EC: 1.1.1.42;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI;
SOURCE 3 ORGANISM_TAXID: 83333;
SOURCE 4 STRAIN: K-12;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS OXIDOREDUCTASE, OXIDATIVE BETA-DECARBOXYLATION
EXPDTA X-RAY DIFFRACTION
AUTHOR S.GONCALVES,S.P.MILLER,M.A.CARRONDO,A.M.DEAN,P.M.MATIAS
REVDAT 2 20-DEC-23 4AJR 1 REMARK LINK
REVDAT 1 31-OCT-12 4AJR 0
JRNL AUTH S.GONCALVES,S.P.MILLER,M.A.CARRONDO,A.M.DEAN,P.M.MATIAS
JRNL TITL INDUCED FIT AND THE CATALYTIC MECHANISM OF ISOCITRATE
JRNL TITL 2 DEHYDROGENASE.
JRNL REF BIOCHEMISTRY V. 51 7098 2012
JRNL REFN ISSN 0006-2960
JRNL PMID 22891681
JRNL DOI 10.1021/BI300483W
REMARK 2
REMARK 2 RESOLUTION. 2.69 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE)
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.69
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.89
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : 23554
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.163
REMARK 3 R VALUE (WORKING SET) : 0.160
REMARK 3 FREE R VALUE : 0.209
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 1195
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 52.9042 - 5.5879 1.00 2686 132 0.1754 0.2007
REMARK 3 2 5.5879 - 4.4360 1.00 2523 135 0.1379 0.1846
REMARK 3 3 4.4360 - 3.8755 1.00 2502 141 0.1311 0.1815
REMARK 3 4 3.8755 - 3.5212 1.00 2461 140 0.1431 0.1899
REMARK 3 5 3.5212 - 3.2689 1.00 2483 127 0.1542 0.2155
REMARK 3 6 3.2689 - 3.0762 1.00 2463 139 0.1702 0.2463
REMARK 3 7 3.0762 - 2.9221 1.00 2450 122 0.1919 0.2493
REMARK 3 8 2.9221 - 2.7949 1.00 2429 140 0.2013 0.2522
REMARK 3 9 2.7949 - 2.6873 0.96 2362 119 0.2269 0.2921
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.10
REMARK 3 SHRINKAGE RADIUS : 0.83
REMARK 3 K_SOL : 0.40
REMARK 3 B_SOL : 27.03
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.660
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.020
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 47.08
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 22.81210
REMARK 3 B22 (A**2) : 22.81210
REMARK 3 B33 (A**2) : 13.92550
REMARK 3 B12 (A**2) : 0.00000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.008 3349
REMARK 3 ANGLE : 1.139 4543
REMARK 3 CHIRALITY : 0.069 503
REMARK 3 PLANARITY : 0.004 582
REMARK 3 DIHEDRAL : 17.288 1264
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4AJR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-FEB-12.
REMARK 100 THE DEPOSITION ID IS D_1290051346.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : ESRF
REMARK 200 BEAMLINE : ID14-4
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.9535
REMARK 200 MONOCHROMATOR : CHANNEL-CUT ESRF MONOCHROMATOR
REMARK 200 OPTICS : TOROIDAL MIRROR
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS
REMARK 200 DATA SCALING SOFTWARE : SCALA
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23556
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.690
REMARK 200 RESOLUTION RANGE LOW (A) : 60.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 8.600
REMARK 200 R MERGE (I) : 0.12000
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.69
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5
REMARK 200 DATA REDUNDANCY IN SHELL : 8.30
REMARK 200 R MERGE FOR SHELL (I) : 0.84000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER
REMARK 200 STARTING MODEL: PDB ENTRY 1AI2
REMARK 200
REMARK 200 REMARK: NONE
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 72.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.50
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.85 M NH4SO4, 50 MM CITRIC
REMARK 280 ACID/NA2HPO4 BUFFER PH 5.2, 0.1 M NACL AND 0.2 M DTT
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-Z+1/2
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.74400
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 52.89400
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 52.89400
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 109.11600
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 52.89400
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 52.89400
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.37200
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 52.89400
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 52.89400
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 109.11600
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 52.89400
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 52.89400
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.37200
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.74400
REMARK 290
REMARK 290 REMARK: NULL
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 12200 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 29660 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.7 KCAL/MOL
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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000
REMARK 400
REMARK 400 COMPOUND
REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LYS 100 TO MET
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 MET A 1
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT
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 OH TYR A 78 OE1 GLU A 87 2.13
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 LEU A 16 77.05 -119.87
REMARK 500 ASN A 18 -117.64 78.61
REMARK 500 LYS A 58 43.39 39.37
REMARK 500 ASP A 81 -17.46 79.78
REMARK 500 ARG A 96 -36.47 74.54
REMARK 500 GLU A 157 -151.03 -130.54
REMARK 500 ASP A 158 -179.35 74.46
REMARK 500 LYS A 230 54.38 -119.32
REMARK 500 MET A 234 74.48 -104.91
REMARK 500 THR A 237 -74.38 -117.83
REMARK 500 ASP A 259 -122.30 58.38
REMARK 500 ASP A 297 -96.21 -137.47
REMARK 500 ALA A 342 70.11 19.18
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE (NAP):
REMARK 600 THIS IS NADPH, THE REDUCED FORM OF NADP
REMARK 600 RIBOSYLNICOTINAMIDE-5'-PHOSPHATE (NMP): THIS IS A NADP
REMARK 600 FRAGMENT FROM HYDROLYSIS
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 MG A1419 MG
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP A 283 OD2
REMARK 620 2 ASP A 307 OD1 98.6
REMARK 620 3 AKG A1418 O2 148.6 83.0
REMARK 620 4 AKG A1418 O5 87.6 78.5 61.9
REMARK 620 5 HOH A2051 O 122.0 74.2 88.7 141.9
REMARK 620 6 HOH A2106 O 84.4 162.4 103.5 119.1 89.5
REMARK 620 N 1 2 3 4 5
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NMN A 504
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAP A 1417
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 1418
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1419
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1AI2 RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND
REMARK 900 CALCIUM (FLASH-COOLED)
REMARK 900 RELATED ID: 1AI3 RELATED DB: PDB
REMARK 900 ORBITAL STEERING IN THE CATALYTIC POWER OF ENZYMES: SMALL
REMARK 900 STRUCTURAL CHANGES WITH LARGE CATALYTIC CONSEQUENCES
REMARK 900 RELATED ID: 1BL5 RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE
REMARK 900 STRUCTURE OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION
REMARK 900 RELATED ID: 1CW1 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF ISOCITRATE DEHYDROGENASE MUTANT K230M BOUND TO
REMARK 900 ISOCITRATE AND MN2+
REMARK 900 RELATED ID: 1CW4 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF K230M ISOCITRATE DEHYDROGENASE IN COMPLEX WITH
REMARK 900 ALPHA- KETOGLUTARATE
REMARK 900 RELATED ID: 1CW7 RELATED DB: PDB
REMARK 900 LOW TEMPERATURE STRUCTURE OF WILD-TYPE IDH COMPLEXED WITH MG-
REMARK 900 ISOCITRATE
REMARK 900 RELATED ID: 1GRO RELATED DB: PDB
REMARK 900 RELATED ID: 1GRP RELATED DB: PDB
REMARK 900 RELATED ID: 1HJ6 RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE S113E MUTANT COMPLEXED WITH
REMARK 900 ISOPROPYLMALATE, NADP+ AND MAGNESIUM (FLASH-COOLED)
REMARK 900 RELATED ID: 1IDC RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE FROM E.COLI (MUTANT K230M), STEADY-STATE
REMARK 900 INTERMEDIATE COMPLEX DETERMINED BY LAUE CRYSTALLOGRAPHY
REMARK 900 RELATED ID: 1IDD RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE Y160F MUTANT APO ENZYME
REMARK 900 RELATED ID: 1IDE RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE Y160F MUTANT STEADY-STATE INTERMEDIATE
REMARK 900 COMPLEX (LAUE DETERMINATION)
REMARK 900 RELATED ID: 1IDF RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE K230M MUTANT APO ENZYME
REMARK 900 RELATED ID: 1IKA RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE COMPLEXED WITH ALPHA-KETOGLUTARATE
REMARK 900 RELATED ID: 1ISO RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE: STRUCTURE OF AN ENGINEERED NADP + --> NAD+
REMARK 900 SPECIFICITY-REVERSAL MUTANT
REMARK 900 RELATED ID: 1P8F RELATED DB: PDB
REMARK 900 A FOUR LOCATION MODEL TO EXPLAIN THE STEREOSPECIFICITY OFPROTEINS.
REMARK 900 RELATED ID: 1PB1 RELATED DB: PDB
REMARK 900 A FOUR LOCATION MODEL TO EXPLAIN THE STEREOSPECIFICITY OFPROTEINS.
REMARK 900 RELATED ID: 1PB3 RELATED DB: PDB
REMARK 900 SITES OF BINDING AND ORIENTATION IN A FOUR LOCATION MODELFOR
REMARK 900 PROTEIN STEREOSPECIFICITY.
REMARK 900 RELATED ID: 1SJS RELATED DB: PDB
REMARK 900 ACCESS TO PHOSPHORYLATION IN ISOCITRATE DEHYDROGENASE MAY OCCUR BY
REMARK 900 DOMAIN SHIFTING
REMARK 900 RELATED ID: 3ICD RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE
REMARK 900 RELATED ID: 4ICD RELATED DB: PDB
REMARK 900 PHOSPHORYLATED ISOCITRATE DEHYDROGENASE
REMARK 900 RELATED ID: 5ICD RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE COMPLEX WITH MG2+ AND ISOCITRATE
REMARK 900 RELATED ID: 6ICD RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE (MUTANT WITH SER 113 REPLACED BY ASP)
REMARK 900 (S113D)
REMARK 900 RELATED ID: 7ICD RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE (MUTANT WITH SER 113 REPLACED BY GLU) (/
REMARK 900 S113E)
REMARK 900 RELATED ID: 8ICD RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE (MUTANT WITH SER 113 REPLACED BY GLU)
REMARK 900 (S113E) COMPLEX WITH MG2+ AND ISOCITRATE
REMARK 900 RELATED ID: 9ICD RELATED DB: PDB
REMARK 900 ISOCITRATE DEHYDROGENASE COMPLEX WITH NADP+
DBREF 4AJR A 1 416 UNP P08200 IDH_ECOLI 1 416
SEQADV 4AJR MET A 100 UNP P08200 LYS 100 ENGINEERED MUTATION
SEQRES 1 A 416 MET GLU SER LYS VAL VAL VAL PRO ALA GLN GLY LYS LYS
SEQRES 2 A 416 ILE THR LEU GLN ASN GLY LYS LEU ASN VAL PRO GLU ASN
SEQRES 3 A 416 PRO ILE ILE PRO TYR ILE GLU GLY ASP GLY ILE GLY VAL
SEQRES 4 A 416 ASP VAL THR PRO ALA MET LEU LYS VAL VAL ASP ALA ALA
SEQRES 5 A 416 VAL GLU LYS ALA TYR LYS GLY GLU ARG LYS ILE SER TRP
SEQRES 6 A 416 MET GLU ILE TYR THR GLY GLU LYS SER THR GLN VAL TYR
SEQRES 7 A 416 GLY GLN ASP VAL TRP LEU PRO ALA GLU THR LEU ASP LEU
SEQRES 8 A 416 ILE ARG GLU TYR ARG VAL ALA ILE MET GLY PRO LEU THR
SEQRES 9 A 416 THR PRO VAL GLY GLY GLY ILE ARG SER LEU ASN VAL ALA
SEQRES 10 A 416 LEU ARG GLN GLU LEU ASP LEU TYR ILE CYS LEU ARG PRO
SEQRES 11 A 416 VAL ARG TYR TYR GLN GLY THR PRO SER PRO VAL LYS HIS
SEQRES 12 A 416 PRO GLU LEU THR ASP MET VAL ILE PHE ARG GLU ASN SER
SEQRES 13 A 416 GLU ASP ILE TYR ALA GLY ILE GLU TRP LYS ALA ASP SER
SEQRES 14 A 416 ALA ASP ALA GLU LYS VAL ILE LYS PHE LEU ARG GLU GLU
SEQRES 15 A 416 MET GLY VAL LYS LYS ILE ARG PHE PRO GLU HIS CYS GLY
SEQRES 16 A 416 ILE GLY ILE LYS PRO CYS SER GLU GLU GLY THR LYS ARG
SEQRES 17 A 416 LEU VAL ARG ALA ALA ILE GLU TYR ALA ILE ALA ASN ASP
SEQRES 18 A 416 ARG ASP SER VAL THR LEU VAL HIS LYS GLY ASN ILE MET
SEQRES 19 A 416 LYS PHE THR GLU GLY ALA PHE LYS ASP TRP GLY TYR GLN
SEQRES 20 A 416 LEU ALA ARG GLU GLU PHE GLY GLY GLU LEU ILE ASP GLY
SEQRES 21 A 416 GLY PRO TRP LEU LYS VAL LYS ASN PRO ASN THR GLY LYS
SEQRES 22 A 416 GLU ILE VAL ILE LYS ASP VAL ILE ALA ASP ALA PHE LEU
SEQRES 23 A 416 GLN GLN ILE LEU LEU ARG PRO ALA GLU TYR ASP VAL ILE
SEQRES 24 A 416 ALA CYS MET ASN LEU ASN GLY ASP TYR ILE SER ASP ALA
SEQRES 25 A 416 LEU ALA ALA GLN VAL GLY GLY ILE GLY ILE ALA PRO GLY
SEQRES 26 A 416 ALA ASN ILE GLY ASP GLU CYS ALA LEU PHE GLU ALA THR
SEQRES 27 A 416 HIS GLY THR ALA PRO LYS TYR ALA GLY GLN ASP LYS VAL
SEQRES 28 A 416 ASN PRO GLY SER ILE ILE LEU SER ALA GLU MET MET LEU
SEQRES 29 A 416 ARG HIS MET GLY TRP THR GLU ALA ALA ASP LEU ILE VAL
SEQRES 30 A 416 LYS GLY MET GLU GLY ALA ILE ASN ALA LYS THR VAL THR
SEQRES 31 A 416 TYR ASP PHE GLU ARG LEU MET ASP GLY ALA LYS LEU LEU
SEQRES 32 A 416 LYS CYS SER GLU PHE GLY ASP ALA ILE ILE GLU ASN MET
HET NMN A 504 22
HET NAP A1417 48
HET AKG A1418 10
HET MG A1419 1
HETNAM NMN BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE
HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
HETNAM AKG 2-OXOGLUTARIC ACID
HETNAM MG MAGNESIUM ION
HETSYN NMN NICOTINAMIDE MONONUCLEOTIDE
HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
FORMUL 2 NMN C11 H16 N2 O8 P 1+
FORMUL 3 NAP C21 H28 N7 O17 P3
FORMUL 4 AKG C5 H6 O5
FORMUL 5 MG MG 2+
FORMUL 6 HOH *127(H2 O)
HELIX 1 1 ILE A 37 LYS A 58 1 22
HELIX 2 2 GLY A 71 GLY A 79 1 9
HELIX 3 3 PRO A 85 ARG A 96 1 12
HELIX 4 4 SER A 113 ASP A 123 1 11
HELIX 5 5 HIS A 143 LEU A 146 5 4
HELIX 6 6 ASP A 158 GLY A 162 5 5
HELIX 7 7 SER A 169 MET A 183 1 15
HELIX 8 8 SER A 202 ASN A 220 1 19
HELIX 9 9 THR A 237 GLY A 254 1 18
HELIX 10 10 ALA A 282 ARG A 292 1 11
HELIX 11 11 PRO A 293 TYR A 296 5 4
HELIX 12 12 MET A 302 VAL A 317 1 16
HELIX 13 13 GLY A 319 ILE A 322 5 4
HELIX 14 14 ALA A 342 ALA A 346 5 5
HELIX 15 15 PRO A 353 MET A 367 1 15
HELIX 16 16 TRP A 369 ALA A 386 1 18
HELIX 17 17 THR A 390 ARG A 395 1 6
HELIX 18 18 LYS A 404 ASN A 415 1 12
SHEET 1 AA12 SER A 64 GLU A 67 0
SHEET 2 AA12 ILE A 28 ILE A 32 1 O ILE A 29 N MET A 66
SHEET 3 AA12 VAL A 97 MET A 100 1 O ILE A 99 N ILE A 32
SHEET 4 AA12 ALA A 333 ALA A 337 1 O ALA A 333 N ALA A 98
SHEET 5 AA12 PRO A 324 ILE A 328 -1 O GLY A 325 N GLU A 336
SHEET 6 AA12 ILE A 126 ARG A 132 -1 O ILE A 126 N ILE A 328
SHEET 7 AA12 ASP A 148 GLU A 154 -1 O MET A 149 N VAL A 131
SHEET 8 AA12 VAL A 298 CYS A 301 1 O ILE A 299 N PHE A 152
SHEET 9 AA12 SER A 224 HIS A 229 1 O SER A 224 N VAL A 298
SHEET 10 AA12 GLU A 274 ILE A 281 1 O VAL A 276 N VAL A 225
SHEET 11 AA12 LEU A 264 LYS A 267 -1 O LEU A 264 N ILE A 277
SHEET 12 AA12 GLU A 256 LEU A 257 -1 O GLU A 256 N LYS A 265
SHEET 1 AB 2 GLU A 164 TRP A 165 0
SHEET 2 AB 2 ILE A 196 GLY A 197 -1 O ILE A 196 N TRP A 165
SHEET 1 AC 2 THR A 388 VAL A 389 0
SHEET 2 AC 2 LYS A 401 LEU A 402 1 O LYS A 401 N VAL A 389
LINK OD2 ASP A 283 MG MG A1419 7555 1555 2.58
LINK OD1 ASP A 307 MG MG A1419 1555 1555 2.35
LINK O2 AKG A1418 MG MG A1419 1555 1555 2.81
LINK O5 AKG A1418 MG MG A1419 1555 1555 2.80
LINK MG MG A1419 O HOH A2051 1555 1555 2.72
LINK MG MG A1419 O HOH A2106 1555 1555 2.50
CISPEP 1 GLY A 261 PRO A 262 0 1.41
SITE 1 AC1 4 ILE A 258 GLY A 261 PRO A 262 TRP A 263
SITE 1 AC2 34 ILE A 37 PRO A 102 LEU A 103 THR A 104
SITE 2 AC2 34 THR A 105 ASN A 115 ASN A 232 ILE A 281
SITE 3 AC2 34 GLN A 288 ARG A 292 ILE A 320 GLY A 321
SITE 4 AC2 34 GLU A 336 THR A 338 HIS A 339 GLY A 340
SITE 5 AC2 34 THR A 341 ALA A 342 LYS A 344 TYR A 345
SITE 6 AC2 34 VAL A 351 ASN A 352 TYR A 391 ASP A 392
SITE 7 AC2 34 AKG A1418 HOH A2044 HOH A2100 HOH A2102
SITE 8 AC2 34 HOH A2103 HOH A2107 HOH A2124 HOH A2125
SITE 9 AC2 34 HOH A2126 HOH A2127
SITE 1 AC3 14 THR A 105 SER A 113 ASN A 115 ARG A 119
SITE 2 AC3 14 ARG A 129 ARG A 153 TYR A 160 LYS A 230
SITE 3 AC3 14 ASP A 307 THR A 338 NAP A1417 MG A1419
SITE 4 AC3 14 HOH A2044 HOH A2094
SITE 1 AC4 6 ASP A 283 ASP A 307 ASP A 311 AKG A1418
SITE 2 AC4 6 HOH A2051 HOH A2106
CRYST1 105.788 105.788 145.488 90.00 90.00 90.00 P 43 21 2 8
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 0.009453 0.000000 0.000000 0.00000
SCALE2 0.000000 0.009453 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006873 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
