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- PDB-2dkb: DIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE ... -

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Basic information

Entry
Database: PDB / ID: 2dkb
TitleDIALKYLGLYCINE DECARBOXYLASE STRUCTURE: BIFUNCTIONAL ACTIVE SITE AND ALKALI METAL BINDING SITES
Components2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)2,2-dialkylglycine decarboxylase (pyruvate)
KeywordsLYASE(DECARBOXYLASE)
Function / homology
Function and homology information


2,2-dialkylglycine decarboxylase (pyruvate) / 2,2-dialkylglycine decarboxylase (pyruvate) activity / L-alanine catabolic process, by transamination / alanine-glyoxylate transaminase activity / glyoxylate catabolic process / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / 2,2-dialkylglycine decarboxylase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsToney, M.D. / Hohenester, E. / Jansonius, J.N.
Citation
Journal: Science / Year: 1993
Title: Dialkylglycine decarboxylase structure: bifunctional active site and alkali metal sites.
Authors: Toney, M.D. / Hohenester, E. / Cowan, S.W. / Jansonius, J.N.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary X-Ray Diffraction Studies of Dialkylglycine Decarboxylase, a Decarboxylating Transaminase
Authors: Toney, M.D. / Keller, J.W. / Pauptit, R.A. / Jaeger, J. / Wise, M.K. / Sauder, U. / Jansonius, J.N.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Pseudomonas Cepacia 2.2-Dialkylglycine Decarboxylase. Sequence and Expression in Escherichia Coli of Structural and Repressor Genes
Authors: Keller, J.W. / Baurick, K.B. / Rutt, G.C. / O'Malley, M.V. / Sonafrank, N.L. / Reynolds, R.A. / Ebbesson, L.O. / Vajdos, F.F.
History
DepositionJul 12, 1994Processing site: BNL
Revision 1.0Oct 15, 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 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0665
Polymers46,5771
Non-polymers4884
Water4,125229
1
A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules

A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,13210
Polymers93,1552
Non-polymers9778
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area12050 Å2
ΔGint-97 kcal/mol
Surface area28410 Å2
MethodPISA
2
A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules

A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules

A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules

A: 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,26320
Polymers186,3104
Non-polymers1,95316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/31
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Buried area29650 Å2
ΔGint-201 kcal/mol
Surface area51250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)152.700, 152.700, 86.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Atom site foot note1: THE FOLLOWING RESIDUES HAVE WEAK ELECTRON DENSITY: 142 - 143, 346 - 347, AND 369 - 377.
2: AT SITE PLP, RESIDUE LYS 272 HAS THE COFACTOR PYRIDOXAL-5'-PHOSPHATE COVALENTLY ATTACHED TO IT.
DetailsDGD IS A TETRAMER OF IDENTICAL SUBUNITS. THE FOLLOWING TRANSFORMATIONS WILL GENERATE THE OTHER THREE SUBUNITS OF THE TETRAMER: MTRIX1 1 -0.500000 0.866010 0.000000 0.00000 MTRIX2 1 0.866041 0.500000 0.000000 0.00000 MTRIX3 1 0.000000 0.000000 -1.000000 28.86753 MTRIX1 2 0.500000 -0.866010 0.000000 76.34753 MTRIX2 2 -0.866041 -0.500000 0.000000 132.24016 MTRIX3 2 0.000000 0.000000 -1.000000 28.86753 MTRIX1 3 -1.000000 0.000000 0.000000 76.34753 MTRIX2 3 0.000000 -1.000000 0.000000 132.24016 MTRIX3 3 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein 2,2-DIALKYLGLYCINE DECARBOXYLASE (PYRUVATE) / 2,2-dialkylglycine decarboxylase (pyruvate)


Mass: 46577.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cepacia (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P16932, 2,2-dialkylglycine decarboxylase (pyruvate)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: DGDA_BURCE SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLN 14 HIS 15 GLU 51 GLN 52 GLY 80 GLU 81 ILE 81 MET 82 VAL 82 LEU 83 ARG 307 PRO 308 PRO 309 LEU 309 GLY 312 ALA 312 THE PUBLISHED AMINO ACID SEQUENCE (REF. 1) WAS CORRECTED AT TWO POSITIONS (J.W. KELLER, PRIVATE COMMUNICATION): RESIDUES 81 - 83: GLY-ILE-VAL TO GLU-MET-LEU. RESIDUES 308 - 313: ARG-CYS-PRO-PRO-ALA-GLY TO -PRO-LEU-PRO-ALA-ALA (INCLUDES A DELETION!). RESIDUE 15 IS HIS AS IN REFERENCE 1. RESIDUE 52 IS GLN (J.W. KELLER, PRIVATE COMMUNICATION). THE FIRST TWO RESIDUES ARE NOT INCLUDED IN THE MODEL SINCE THEY ARE DISORDERED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.67 %
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Details: taken from Toney, M.D., (1991) J.Mol.Biol., 222, 873.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120-60 mg/mlprotein1drop
25 mMpotassium phosphate1drop
30.015 mMPLP1drop
40.02 %(w/v)sodium azide1drop
515 mMmorpholinoethanesulfonic acid1reservoir
615 %(w/v)PEG40001reservoir
8150 mMsodium pyruvate1reservoir
90.015 mMPLP1reservoir
7potassium hydroxide1reservoirto neutralize
100.02 %sodium azide1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 32665 / % possible obs: 93 % / Rmerge(I) obs: 0.078

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 2.1→8 Å / Rfactor obs: 0.178
Details: ATOMS THAT ARE NOT WELL DEFINED DUE TO POOR ELECTRON DENSITY OR REFINE TO B-FACTORS (GREATER THAN) 100 ANGSTROMS**2 HAVE A WEIGHT OF ZERO.
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 29 229 3510
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_angle_deg2.2
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_d2.2
X-RAY DIFFRACTIONt_plane_restr0.008

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