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- PDB-2pv7: Crystal structure of chorismate mutase / prephenate dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 2pv7
TitleCrystal structure of chorismate mutase / prephenate dehydrogenase (tyrA) (1574749) from Haemophilus influenzae RD at 2.00 A resolution
ComponentsT-protein [Includes: Chorismate mutase (EC 5.4.99.5) (CM) and Prephenate dehydrogenase (EC 1.3.1.12) (PDH)]
KeywordsISOMERASE / OXIDOREDUCTASE / 1574749 / Chorismate mutase type II / chorismate mutase / prephenate dehydrogenase (tyrA) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


prephenate dehydrogenase / prephenate dehydrogenase (NADP+) activity / prephenate dehydrogenase (NAD+) activity / tyrosine biosynthetic process / chorismate metabolic process / chorismate mutase / chorismate mutase activity / : / NAD+ binding / cytoplasm
Similarity search - Function
Bifunctional chorismate mutase/prephenate dehydrogenase T-protein / Chorismate mutase, T-protein / 6-phosphogluconate dehydrogenase C-terminal fold / 6-phosphogluconate dehydrogenase C-terminal like domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / Chorismate mutase domain superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II ...Bifunctional chorismate mutase/prephenate dehydrogenase T-protein / Chorismate mutase, T-protein / 6-phosphogluconate dehydrogenase C-terminal fold / 6-phosphogluconate dehydrogenase C-terminal like domain / Prephenate dehydrogenase / Prephenate dehydrogenase, nucleotide-binding domain / Prephenate/arogenate dehydrogenase domain profile. / Chorismate mutase domain superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TYROSINE / T-protein
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: The structure of Haemophilus influenzae prephenate dehydrogenase suggests unique features of bifunctional TyrA enzymes.
Authors: Chiu, H.J. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / ...Authors: Chiu, H.J. / Abdubek, P. / Astakhova, T. / Axelrod, H.L. / Carlton, D. / Clayton, T. / Das, D. / Deller, M.C. / Duan, L. / Feuerhelm, J. / Grant, J.C. / Grzechnik, A. / Han, G.W. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Kozbial, P. / Krishna, S.S. / Kumar, A. / Marciano, D. / McMullan, D. / Miller, M.D. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Reyes, R. / Tien, H.J. / Trame, C.B. / van den Bedem, H. / Weekes, D. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Elsliger, M.A. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionMay 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THIS CONSTRUCT IS COMPRISED OF AMINO ACIDS 81-377 OF THE FULL-LENGTH PROTEIN (1-377) AND ... SEQUENCE THIS CONSTRUCT IS COMPRISED OF AMINO ACIDS 81-377 OF THE FULL-LENGTH PROTEIN (1-377) AND WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-protein [Includes: Chorismate mutase (EC 5.4.99.5) (CM) and Prephenate dehydrogenase (EC 1.3.1.12) (PDH)]
B: T-protein [Includes: Chorismate mutase (EC 5.4.99.5) (CM) and Prephenate dehydrogenase (EC 1.3.1.12) (PDH)]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2416
Polymers68,5522
Non-polymers1,6894
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13350 Å2
ΔGint-109 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.790, 127.790, 100.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-512-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYALAAA92 - 37113 - 292
21GLYALABB92 - 37113 - 292
32NADTYRAE - C400 - 4011
42NADTYRBF - D400 - 4011
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein T-protein [Includes: Chorismate mutase (EC 5.4.99.5) (CM) and Prephenate dehydrogenase (EC 1.3.1.12) (PDH)]


Mass: 34275.805 Da / Num. of mol.: 2 / Fragment: Residues 81-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd, DSM 11121, KW20 / Gene: 1574749, tyrA, HI1290 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
References: UniProt: P43902, chorismate mutase, prephenate dehydrogenase
#2: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO3
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 0.04M Potassium dihydrogen phosphate, 20.0% Glycerol, 16.0% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 8, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97921
ReflectionResolution: 2→29.696 Å / Num. obs: 56593 / % possible obs: 99.7 % / Redundancy: 7.29 % / Biso Wilson estimate: 32.83 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.89
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
2-2.070.5072.56395849589199.3
2.07-2.150.3743.5399639827194.1
2.15-2.250.2864.54239610550195.5
2.25-2.370.2365.54183110490196.4
2.37-2.520.1667.74201410610197.4
2.52-2.710.1369.24073010322197.8
2.71-2.990.09512.94250610884198.8
2.99-3.420.05719.44126110594199.1
3.42-4.30.03529.34116410659199.6
4.3-29.70.02834.440875198

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.696 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.931 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.121
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. RESIDUES 81-91, 312-315, 372-377 IN CHAIN A AND 81-91, 372-377 IN CHAIN B ARE DISORDERED AND ARE NOT MODELED. 5. LIGAND MOLECULES NAD AND TYR ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.194 2870 5.1 %RANDOM
Rwork0.161 ---
all0.163 ---
obs0.163 56541 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2→29.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4427 0 114 393 4934
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224699
X-RAY DIFFRACTIONr_bond_other_d0.0010.024282
X-RAY DIFFRACTIONr_angle_refined_deg1.611.986396
X-RAY DIFFRACTIONr_angle_other_deg0.939921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6215569
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47124.081223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80115797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3771529
X-RAY DIFFRACTIONr_chiral_restr0.0940.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025168
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02959
X-RAY DIFFRACTIONr_nbd_refined0.2060.2944
X-RAY DIFFRACTIONr_nbd_other0.1770.24245
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22268
X-RAY DIFFRACTIONr_nbtor_other0.0850.22449
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1040.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2250.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.214
X-RAY DIFFRACTIONr_mcbond_it2.18932918
X-RAY DIFFRACTIONr_mcbond_other0.58631148
X-RAY DIFFRACTIONr_mcangle_it2.96154495
X-RAY DIFFRACTIONr_scbond_it4.92682094
X-RAY DIFFRACTIONr_scangle_it6.309111893
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4218 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.225
LOOSE THERMAL1.7610
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 220 -
Rwork0.226 3883 -
obs-4103 99.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.19750.58110.00681.4205-0.09321.44250.0102-0.5122-0.4070.1744-0.0109-0.03260.3335-0.12430.00080.0494-0.005-0.01580.09210.11490.03455.829531.182457.6504
20.31120.08490.05471.23830.53150.95260.02380.0344-0.06020.10570.1215-0.16050.06070.181-0.1453-0.11580.0509-0.0343-0.0212-0.0542-0.032528.787253.328350.68
30.72080.02770.53240.94210.11070.63590.04180.02770.1759-0.16310.17930.13310.05770.0548-0.2211-0.14680.0267-0.0127-0.0934-0.0322-0.085715.466455.161243.5727
40.8152-0.2090.0471.2806-0.40611.25630.00030.0870.05420.04490.033-0.0605-0.29570.1396-0.0333-0.0186-0.05590.0465-0.0471-0.0115-0.09324.723185.878742.4968
50.38840.0170.03430.89010.04420.5169-0.03960.0368-0.06050.02830.1251-0.12150.0330.1277-0.0855-0.11450.0262-0.0023-0.0276-0.0571-0.047329.415154.502548.6925
60.0643-0.0267-0.01221.7558-0.4751.5139-0.0412-0.0025-0.08140.24850.0930.10460.1316-0.0717-0.0518-0.12670.03170.0078-0.0618-0.0418-0.092418.714460.476257.3256
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA92 - 24713 - 168
22AA248 - 349169 - 270
33AA350 - 371271 - 292
43AE - C400 - 4011
54BB92 - 24913 - 170
65BB250 - 347171 - 268
76BB348 - 371269 - 292
86BF - D400 - 4011

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