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- PDB-2mnr: MECHANISM OF THE REACTION CATALYZED BY MANDELATE RACEMASE. 2. CRY... -

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Entry
Database: PDB / ID: 2mnr
TitleMECHANISM OF THE REACTION CATALYZED BY MANDELATE RACEMASE. 2. CRYSTAL STRUCTURE OF MANDELATE RACEMASE AT 2.5 ANGSTROMS RESOLUTION: IDENTIFICATION OF THE ACTIVE SITE AND POSSIBLE CATALYTIC RESIDUES
ComponentsMANDELATE RACEMASE
KeywordsRACEMASE
Function / homology
Function and homology information


mandelate racemase / mandelate racemase activity / mandelate catabolic process / amino acid catabolic process / hydro-lyase activity / metal ion binding
Similarity search - Function
Mandelate racemase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like ...Mandelate racemase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Mandelate racemase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsNeidhart, D.J. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 1991
Title: Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues.
Authors: Neidhart, D.J. / Howell, P.L. / Petsko, G.A. / Powers, V.M. / Li, R.S. / Kenyon, G.L. / Gerlt, J.A.
#1: Journal: Nature / Year: 1990
Title: Mandelate Racemase and Muconate Lactonizing Enzyme are Mechanistically Distinct and Structurally Homologous
Authors: Neidhart, D.J. / Kenyon, G.L. / Gerlt, J.A. / Petsko, G.A.
History
DepositionJul 6, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.5Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.7Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET BETA SHEETS ARE NAMED FOR THE MAJOR DOMAINS IN WHICH THEY OCCUR: "N" FOR N-TERMINAL DOMAIN, ...SHEET BETA SHEETS ARE NAMED FOR THE MAJOR DOMAINS IN WHICH THEY OCCUR: "N" FOR N-TERMINAL DOMAIN, "B" FOR BETA-BARREL DOMAIN, AND "C" FOR C-TERMINAL DOMAIN. "F" REFERS TO THE ACTIVE SITE FLAP. LIKEWISE, ALPHA HELICES ARE NAMED WITH TWO CHARACTERS, THE FIRST REFERRING TO THE DOMAIN IN WHICH THEY OCCUR. THE SHEET PRESENTED AS *B* ON SHEET RECORDS BELOW IS ACTUALLY AN EIGHT-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MANDELATE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5353
Polymers38,3841
Non-polymers1512
Water3,801211
1
A: MANDELATE RACEMASE
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)308,28324
Polymers307,0758
Non-polymers1,20816
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area28870 Å2
ΔGint-350 kcal/mol
Surface area84750 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.000, 125.000, 106.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

21A-598-

HOH

31A-612-

HOH

41A-614-

HOH

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Components

#1: Protein MANDELATE RACEMASE /


Mass: 38384.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / References: UniProt: P11444, mandelate racemase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMANDELATE RACEMASE ABSOLUTELY REQUIRES A DIVALENT METAL ION FOR ACTIVITY AND IS MOST ACTIVE WITH A ...MANDELATE RACEMASE ABSOLUTELY REQUIRES A DIVALENT METAL ION FOR ACTIVITY AND IS MOST ACTIVE WITH A MAGNESIUM (II) ION BOUND IN THE ACTIVE SITE. IN THIS CRYSTAL STRUCTURE, MANGANESE (II) WAS EXCHANGED INTO THE ACTIVE SITE IN ORDER TO FACILITATE X-RAY REFINEMENT OF THE POSITION OF THE BOUND METAL ION. MANGANESE (II) SUBSTITUTED MANDELATE RACEMASE IS ABOUT 48% AS ACTIVE AS HOLOENZYME CONTAINING MAGNESIUM (II); HOWEVER, VERY LITTLE STRUCTURAL CHANGE OF THE ENZYME IS APPARENT BETWEEN THESE FORMS. GIVEN THE MUCH HIGHER NATURAL ABUNDANCE OF MAGNESIUM (II) VS. MANGANESE (II), IT IS LIKELY THAT MAGNESIUM (II) IS THE PREDOMINANT COFACTOR FOR MANDELATE RACEMASE IN VIVO.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140 mg/mlenzyme 1drop
250 mg/mlTris-HCl1drop
310 mg/ml1dropMgCl2
40.01 %1dropNaN3
530 %satammonium sulfate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 9999 Å / Num. obs: 4799 / Observed criterion σ(I): 2 / Num. measured all: 9494 / Rmerge(I) obs: 0.064

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.162 -
obs0.162 25592
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 6 211 2915
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 5 Å / Num. reflection obs: 25592 / σ(F): 1 / Rfactor obs: 0.183 / Rfactor Rwork: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d0.053
X-RAY DIFFRACTIONx_bond_d0.015

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