[English] 日本語
Yorodumi
- SASDD39: Medium load concentration of apo alpha-aminoadipic semialdehyde d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: SASBDB / ID: SASDD39
SampleMedium load concentration of apo alpha-aminoadipic semialdehyde dehydrogenase (ALDH7A1) collected by SEC-SAXS
  • Alpha-aminoadipic semialdehyde dehydrogenase (protein), ALDH7A1, Homo sapiens
Function / homology
Function and homology information


L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / Lysine catabolism / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase (NAD+) activity / glycine betaine biosynthetic process from choline / aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / Lysine catabolism / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase (NAD+) activity / glycine betaine biosynthetic process from choline / aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity / sensory perception of sound / mitochondrial matrix / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
Aldehyde dehydrogenase family 7 member A1-like / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
CitationJournal: FEBS Lett / Year: 2018
Title: NAD promotes assembly of the active tetramer of aldehyde dehydrogenase 7A1.
Authors: David A Korasick / Tommi A White / Srinivas Chakravarthy / John J Tanner /
Abstract: Nicotinamide adenine dinucleotide (NAD) is the redox cofactor of many enzymes, including the vast aldehyde dehydrogenase (ALDH) superfamily. Although the function of NAD(H) in hydride transfer is ...Nicotinamide adenine dinucleotide (NAD) is the redox cofactor of many enzymes, including the vast aldehyde dehydrogenase (ALDH) superfamily. Although the function of NAD(H) in hydride transfer is established, its influence on protein structure is less understood. Herein, we show that NAD -binding promotes assembly of the ALDH7A1 tetramer. Multiangle light scattering, small-angle X-ray scattering, and sedimentation velocity all show a pronounced shift of the dimer-tetramer equilibrium toward the tetramer when NAD is present. Furthermore, electron microscopy shows that cofactor binding enhances tetramer formation even at the low enzyme concentration used in activity assays, suggesting the tetramer is the active species. Altogether, our results suggest that the catalytically active oligomer of ALDH7A1 is assembled on demand in response to cofactor availability.
Contact author
  • David Korasick (Mizzou, University of Missouri-Columbia, Columbia, MO, USA)

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Models

Model #2111
Type: atomic / Chi-square value: 1.23592628292
Search similar-shape structures of this assembly by Omokage search (details)
Model #2112
Type: atomic / Chi-square value: 1.00194886871
Search similar-shape structures of this assembly by Omokage search (details)
Model #2113
Type: atomic / Chi-square value: 1.00194886871
Search similar-shape structures of this assembly by Omokage search (details)

-
Sample

SampleName: Medium load concentration of apo alpha-aminoadipic semialdehyde dehydrogenase (ALDH7A1) collected by SEC-SAXS
BufferName: 50 mM Tris, 50 mM NaCl, 0.5 mM DTT, 5% (v/v) glycerol / pH: 7.8
Entity #1149Name: ALDH7A1 / Type: protein / Description: Alpha-aminoadipic semialdehyde dehydrogenase / Formula weight: 55.56 / Num. of mol.: 4 / Source: Homo sapiens / References: UniProt: P49419
Sequence: GHMSTLLINQ PQYAWLKELG LREENEGVYN GSWGGRGEVI TTYCPANNEP IARVRQASVA DYEETVKKAR EAWKIWADIP APKRGEIVRQ IGDALREKIQ VLGSLVSLEM GKILVEGVGE VQEYVDICDY AVGLSRMIGG PILPSERSGH ALIEQWNPVG LVGIITAFNF ...Sequence:
GHMSTLLINQ PQYAWLKELG LREENEGVYN GSWGGRGEVI TTYCPANNEP IARVRQASVA DYEETVKKAR EAWKIWADIP APKRGEIVRQ IGDALREKIQ VLGSLVSLEM GKILVEGVGE VQEYVDICDY AVGLSRMIGG PILPSERSGH ALIEQWNPVG LVGIITAFNF PVAVYGWNNA IAMICGNVCL WKGAPTTSLI SVAVTKIIAK VLEDNKLPGA ICSLTCGGAD IGTAMAKDER VNLLSFTGST QVGKQVGLMV QERFGRSLLE LGGNNAIIAF EDADLSLVVP SALFAAVGTA GQRCTTARRL FIHESIHDEV VNRLKKAYAQ IRVGNPWDPN VLYGPLHTKQ AVSMFLGAVE EAKKEGGTVV YGGKVMDRPG NYVEPTIVTG LGHDASIAHT ETFAPILYVF KFKNEEEVFA WNNEVKQGLS SSIFTKDLGR IFRWLGPKGS DCGIVNVNIP TSGAEIGGAF GGEKHTGGGR ESGSDAWKQY MRRSTCTINY SKDLPLAQGI KFQ

-
Experimental information

BeamInstrument name: Advanced Photon Source (APS) BioCAT 18ID / City: Argonne, IL / 国: USA / Type of source: X-ray synchrotron / Wavelength: 0.103 Å / Dist. spec. to detc.: 3.5 mm
DetectorName: Pilatus 100K / Pixsize x: 172 mm
Scan
Title: Medium load concentration of apo alpha-aminoadipic semialdehyde dehydrogenase (ALDH7A1) collected by SEC-SAXS
Measurement date: Feb 22, 2018 / Cell temperature: 22 °C / Exposure time: 0.5 sec. / Unit: 1/A /
MinMax
Q0.0054 0.387
ResultType of curve: sec
Comments: Column type: Wyatt WTC 030 S5; flow rate: 0.8 mL/min; injection volume: 250 - 500 µL
ExperimentalPorod
MW149.8 kDa-
Volume-229 nm3

GuinierGuinier error
Forward scattering, I0105.2 0.6
Radius of gyration, Rg3.74 nm0.03

MinMax
Guinier point1 99

+
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://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