[English] 日本語
Yorodumi
- PDB-1mae: The Active Site Structure of Methylamine Dehydrogenase: Hydrazine... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mae
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
NITROGEN MOLECULE / Methylamine dehydrogenase light chain / Methylamine dehydrogenase heavy chain
Similarity search - Component
Biological speciesParacoccus versutus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.8 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 Thiobacillus 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
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / struct_site
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_leaving_atom_flag / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,7143
Polymers51,6862
Non-polymers281
Water1,53185
1
L: METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)
H: METHYLAMINE DEHYDROGENASE (HEAVY SUBUNIT)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)103,4286
Polymers103,3724
Non-polymers562
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
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

-
Components

#1: Protein METHYLAMINE DEHYDROGENASE (LIGHT SUBUNIT)


Mass: 13654.172 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: Chemical ChemComp-HDZ / NITROGEN MOLECULE


Mass: 28.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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 TRP57:CE3-TRP108:CD1 BOND. IN NATIVE MADH TRP57 CONTAINS AN ORTHO-QUINONE FUNCTION ATTACHED TO ATOMS CH2 AND CZ2.
Sequence detailsFOR THE H-SUBUNIT THE SEQUENCE GIVEN IN THE SEQRES RECORDS IS AN *X-RAY SEQUENCE*, WHICH WAS ...FOR THE H-SUBUNIT THE SEQUENCE GIVEN IN THE SEQRES RECORDS IS AN *X-RAY SEQUENCE*, WHICH WAS ESTABLISHED ON THE BASIS OF THE ELECTRON DENSITY DUE TO THE LACK OF AN AMINO ACID SEQUENCE. ONLY CARBON ALPHA COORDINATES ARE PROVIDED FOR THE H-SUBUNIT IN THIS ENTRY. THE ASSIGNMENT OF THE DISULFIDE BRIDGE IN THE H-SUBUNIT IS TENTATIVE. REFINEMENT OF THE MADH MODEL HAS NOT YET BEEN COMPLETED. 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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 4.91 Å3/Da / Density % sol: 74.93 %
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

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 25377 / % possible obs: 95.7 % / Num. measured all: 125106 / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 92.4 % / Rmerge(I) obs: 0.157

-
Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.183 / Highest resolution: 2.8 Å
Details: ALTHOUGH CLEAR EXTRA DENSITY WAS OBSERVED IN THE ACTIVE SITE, SUFFICIENT DENSITY WAS NOT PRESENT TO ACCOMMODATE THE COMPLETE INHIBITOR (FOR DETAILS SEE ARTICLE SPECIFIED IN REFERENCE 1). TWO ...Details: ALTHOUGH CLEAR EXTRA DENSITY WAS OBSERVED IN THE ACTIVE SITE, SUFFICIENT DENSITY WAS NOT PRESENT TO ACCOMMODATE THE COMPLETE INHIBITOR (FOR DETAILS SEE ARTICLE SPECIFIED IN REFERENCE 1). TWO ATOMS OF THE INHIBITOR (MHZ), TENTATIVELY IDENTIFIED AS NITROGENS HAVE BEEN INCLUDED IN THE MODEL AS HDZ.
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1324 0 2 85 1411
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.018
X-RAY DIFFRACTIONt_angle_deg2.8
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more