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- PDB-1ebh: OCTAHEDRAL COORDINATION AT THE HIGH AFFINITY METAL SITE IN ENOLAS... -

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Basic information

Entry
Database: PDB / ID: 1ebh
TitleOCTAHEDRAL COORDINATION AT THE HIGH AFFINITY METAL SITE IN ENOLASE; CRYSTALLOGRAPHIC ANALYSIS OF THE MG++-ENZYME FROM YEAST AT 1.9 ANGSTROMS RESOLUTION
ComponentsENOLASE
KeywordsCARBON-OXYGEN LYASE
Function / homology
Function and homology information


Gluconeogenesis / regulation of vacuole fusion, non-autophagic / Glycolysis / melatonin binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type vacuole / glycolytic process / magnesium ion binding ...Gluconeogenesis / regulation of vacuole fusion, non-autophagic / Glycolysis / melatonin binding / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / fungal-type vacuole / glycolytic process / magnesium ion binding / mitochondrion / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like C-terminal domain ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / 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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWedekind, J.E. / Reed, G.H. / Rayment, I.
Citation
Journal: Biochemistry / Year: 1995
Title: Octahedral coordination at the high-affinity metal site in enolase: crystallographic analysis of the MgII--enzyme complex from yeast at 1.9 A resolution.
Authors: Wedekind, J.E. / Reed, G.H. / Rayment, I.
#1: Journal: Biochemistry / Year: 1994
Title: Chelation of Ser 39 to Mg++ Latches a Gate at the Active Site of Enolase: Structure of the Bis Mg++ Complex of Yeast Enolase and the Intermediate, Phosphonoacetohydroxamate, at 2.1 Angstroms Resolution
Authors: Wedekind, J.E. / Reed, G.H. / Rayment, I.
History
DepositionNov 1, 1994Processing site: BNL
Revision 1.0Apr 27, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 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.ptnr1_label_seq_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.ptnr3_label_seq_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 THE SHEETS PRESENTED AS *BAA* AND *BAB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *BAA* AND *BAB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THESE ARE REPRESENTED BY NINE-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENOLASE
B: ENOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5856
Polymers93,4662
Non-polymers1204
Water9,134507
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-43 kcal/mol
Surface area29540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.500, 73.200, 89.100
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 143 / 2: CIS PROLINE - PRO B 143
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.49366, -1.0E-5, -0.86965), (0.00043, -1, 0.00026), (-0.86965, -0.00051, -0.49366)
Vector: 25.13222, 0.01812, 43.13784)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN A WHEN APPLIED TO CHAIN B. THIS TRANSFORMATION IS A TWO-FOLD OPERATION AND TRANSLATION THAT DESCRIBE THE APPROXIMATE NON-CRYSTALLOGRAPHIC DYAD. THE CRYSTALLOGRAPHICALLY INDEPENDENT UNIT IS ONE DIMER OF CHEMICALLY IDENTICAL SUBUNITS.

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Components

#1: Protein ENOLASE


Mass: 46732.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00924, phosphopyruvate hydratase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 507 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS STRUCTURE COMPLEMENTS THE STUDY OF ENOLASE-BIS(MG)II-PHAH AND SERVES AS A CONTROL EXPERIMENT ...THIS STRUCTURE COMPLEMENTS THE STUDY OF ENOLASE-BIS(MG)II-PHAH AND SERVES AS A CONTROL EXPERIMENT IN THE ABSENCE OF INHIBITOR. THE ACTIVE SITE LOOP (APPROXIMATELY RESIDUES 35 - 43) HAS BEEN MODELED IN THE "OPEN" AND "CLOSED" CONFORMATIONS FOR RESIDUES A 34 - N A 38 AND RESIDUES B 35 - N B 38. THE CLOSED CONFORMATION IS DENOTED AS ALTERNATE CONFORMATION C IN THE ATOM RECORDS BELOW AND THE OPEN CONFORMATION IS DENOTED AS A IN THE ATOM RECORDS BELOW. ADDITIONAL ELECTRON DENSITY FOR THE SIDE CHAINS OF THR A 40 AND THR B 40 WAS MODELED AS SOLVENT.
Nonpolymer detailsMETALS ARE HEXACOORDINATE WITH OCTAHEDRAL GEOMETRY. A CHLORIDE ION IS BOUND AT THE PHOSPHATE ...METALS ARE HEXACOORDINATE WITH OCTAHEDRAL GEOMETRY. A CHLORIDE ION IS BOUND AT THE PHOSPHATE BINDING SITE OF EACH SUBUNIT AND MAKES SPECIFIC CONTACTS TO THE GUANIDINIUM GROUP OF ARG 374 AND THE AMIDE HYDROGEN OF SER 375. IN MUCH OF THE PREVIOUS LITERATURE ON ENOLASE, THE METAL ION WHICH BINDS TIGHTLY TO ENOLASE IN THE ABSENCE OF SUBSTRATES HAS BEEN CALLED THE "CONFORMATIONAL" METAL. THE SECOND METAL ION WHICH BINDS TO ENOLASE IN THE PRESENCE OF THE SUBSTRATE HAS BEEN CALLED THE "CATALYTIC" METAL ION. THE AUTHORS WILL REFER TO THE TWO DIVALENT CATIONS IN ORDER OF DECREASING BINDING AFFINITY AS METAL I AND METAL II, RESPECTIVELY.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growDetails: CRYSTALS WERE GROWN FROM POLYETHYLENE GLYCOL, KCL, AT PH 8.1. CRYSTALLIZED IN THE PRESENCE OF 0.5 MILLIMOLAR MG2+
Crystal grow
*PLUS
pH: 8 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %(w/w)PEG800011
20.25 M11KCl
30.04 MHEPPS11
40.5 mM11MgCl2

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Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 100 Å / Num. obs: 53410 / % possible obs: 75 % / Num. measured all: 77897 / Rmerge(I) obs: 0.041
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2.02 Å / Num. unique obs: 6194 / Num. measured obs: 6392 / Rmerge(I) obs: 0.29

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
CHAINrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.9→50 Å / σ(F): 0
Details: OCCUPANCIES FOR RESIDUES EXHIBITING DUAL CONFORMATIONS HAVE TOTAL OCCUPANCIES OF 1.0 WITH THE FOLLOWING EXCEPTION. ALA A 38 AND ALA B 38 WERE MODELED IN THE OPEN CONFORMATION ONL AFTER ATOM ...Details: OCCUPANCIES FOR RESIDUES EXHIBITING DUAL CONFORMATIONS HAVE TOTAL OCCUPANCIES OF 1.0 WITH THE FOLLOWING EXCEPTION. ALA A 38 AND ALA B 38 WERE MODELED IN THE OPEN CONFORMATION ONL AFTER ATOM N ALA 38 IN EACH CHAIN. THE TOTAL OCCUPANCIES FOR ATOMS OF THIS RESIDUE TOTAL 0.7.
RfactorNum. reflection
obs0.19 53410
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6627 0 4 507 7138
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.2
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 34 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.019
X-RAY DIFFRACTIONp_angle_d2.2

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