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- PDB-2mad: THE ACTIVE SITE STRUCTURE OF METHYLAMINE DEHYDROGENASE: HYDRAZINE... -

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Basic information

Entry
Database: PDB / ID: 2mad
TitleTHE ACTIVE SITE STRUCTURE OF METHYLAMINE DEHYDROGENASE: HYDRAZINES IDENTIFY C6 AS THE REACTIVE SITE OF THE TRYPTOPHAN DERIVED QUINONE COFACTOR
Components
  • METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
  • METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
KeywordsOXIDOREDUCTASE(CHNH2(D)-DEAMINATING)
Function / homology
Function and homology information


methylamine dehydrogenase (amicyanin) / methylamine dehydrogenase (amicyanin) activity / methylamine metabolic process / aliphatic amine dehydrogenase activity / amine metabolic process / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain ...Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain / Amine dehydrogenase heavy chain / Methylamine/Aralkylamine dehydrogenase light chain, C-terminal domain / Amine dehydrogenase light chain / Methylamine/Aralkylamine dehydrogenase light chain superfamily / Methylamine dehydrogenase, L chain / Methylamine dehydrogenase heavy chain (MADH) / Electron Transport Ethylamine Dehydrogenase / Methylamine/Aralkylamine dehydrogenase light chain / Quinoprotein amine dehydrogenase, beta chain-like / WD40/YVTN repeat-like-containing domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesParacoccus versutus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsHuizinga, E.G. / Vellieux, F.M.D. / Hol, W.G.J.
Citation
Journal: Biochemistry / Year: 1992
Title: Active site structure of methylamine dehydrogenase: hydrazines identify C6 as the reactive site of the tryptophan-derived quinone cofactor.
Authors: Huizinga, E.G. / van Zanten, B.A. / Duine, J.A. / Jongejan, J.A. / Huitema, F. / Wilson, K.S. / Hol, W.G.
#1: Journal: FEBS Lett. / Year: 1991
Title: Crystallographic Investigations of the Tryptophan-Derived Cofactor in the Quinoprotein Methylamine Dehydrogenase
Authors: Chen, L. / Mathews, F.S. / Davidson, V.L. / Huizinga, E.G. / Vellieux, F.M.D. / Duine, J.A. / Hol, W.G.J.
#2: Journal: Embo J. / Year: 1989
Title: Structure of Quinoprotein Methylamine Dehydrogenase at 2.25 Angstroms Resolution
Authors: Vellieux, F.M.D. / Huitema, F. / Groendijk, H. / Kalk, K.H. / Frank, J. / Jongejan, J.A. / Duine, J.A. / Petratos, K. / Drenth, J. / Hol, W.G.J.
#3: Journal: Eur.J.Biochem. / Year: 1986
Title: Purification, Crystallization and Preliminary X-Ray Investigation of Quinoprotein Methylamine Dehydrogenase from Thiobacillius Versutus
Authors: Vellieux, F.M.D. / Frank, J. / Swarte, M.B.A. / Groendijk, H. / Duine, J.A. / Drenth, J. / Hol, W.G.J.
History
DepositionMay 20, 1992Processing site: BNL
SupersessionJan 31, 1994ID: 1MAD
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
H: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)51,7002
Polymers51,7002
Non-polymers00
Water1,54986
1
L: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
H: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)

L: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
H: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)


Theoretical massNumber of molelcules
Total (without water)103,4004
Polymers103,4004
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557y,x,-z+21
Unit cell
Length a, b, c (Å)129.784, 129.784, 104.334
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: THE QUINONE CONTAINING TRYPTOPHAN (L 57).THE QUINONE OXYGEN IS GIVEN IN HETATM QTR.
2: LYS L 129 - ALA L 130 OMEGA ANGLE = 0.904 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
DetailsTHE MOLECULE IS NORMALLY A TETRAMER. THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONSISTS OF ONE-HALF OF THE TETRAMER, NAMELY ONE LIGHT CHAIN *L* AND ONE HEAVY CHAIN *H*. TO GENERATE THE FULL MOLECULE, THE FOLLOWING CRYSTALLOGRAPHIC TWO-FOLD OPERATION MUST BE APPLIED TO THE LIGHT AND HEAVY CHAINS PRESENTED IN THIS ENTRY -0.5 0.866025 0.0 0.0 0.866025 0.5 0.0 0.0 0.0 0.0 -1.0 208.368

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Components

#1: Protein METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)


Mass: 13668.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus versutus (bacteria) / References: UniProt: P22641, EC: 1.4.99.3
#2: Protein METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT) / Coordinate model: Cα atoms only


Mass: 38031.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus versutus (bacteria) / References: UniProt: P23006, EC: 1.4.99.3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE L SUBUNIT CONTAINS THE SIDE CHAIN DERIVED COFACTOR TRYPTOPHYL TRYTOPHAN-QUINONE (MCINTYRE ET AL. ...THE L SUBUNIT CONTAINS THE SIDE CHAIN DERIVED COFACTOR TRYPTOPHYL TRYTOPHAN-QUINONE (MCINTYRE ET AL. SCIENCE 252, 1-7) MADE UP OF TWO TRYPTOPHANS WHICH ARE AT POSITIONS 57 AND 108. THESE ARE COVALENTLY LINKED THROUGH A CE3 TRP 57 - CD1 TRP 108 BOND. TRP57 CONTAINS AN ORTHO-QUINONE FUNCTION ATTACHED TO ATOMS CH2 AND CZ2.
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: DMHL_PARDE SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE VAL 71 GLN 14

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.9 Å3/Da / Density % sol: 74.92 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Details: taken from Ubbink, M. et al (1991). Eur. J. Biochem., 202, 1003-1012.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
20.1 Msodium acetate1drop
337-42 %satammonium sulfate1reservoir
40.1 Msodium acetate1reservoir

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.209 / Highest resolution: 2.25 Å
Refinement stepCycle: LAST / Highest resolution: 2.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1325 0 0 86 1411
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg3
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
Highest resolution: 2.25 Å / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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