PDBsum entry 3rtc

Lyase

PDB id: 3rtc

Contents

Protein chain

489 a.a.

Ligands

ALA-PRO-ALA-TRP-LEU-PHE-GLU-ALA

NAD ×2

ATP

Metals

__K

_MG

Waters ×125

PDB id:

3rtc

Name:

Lyase

Title:

Crystal structure of tm0922, a fusion of a domain of unknown function and adp/atp-dependent NAD(p)h-hydrate dehydratase from thermotoga maritima soaked with NAD and atp.

Structure:

Putative uncharacterized protein. Chain: a. Engineered: yes. Unknown peptide, probably from expression host. Chain: b

Source:

Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: tm0922, tm_0922. Expressed in: escherichia coli. Expression_system_taxid: 469008. Escherichia coli. Organism_taxid: 469008. Strain: bl21(de3).

Resolution:

2.10Å R-factor: 0.171 R-free: 0.209

Authors:

I.A.Shumilin,M.Cymborowski,S.A.Lesley,W.Minor

Key ref:

I.A.Shumilin et al. (2012). Identification of unknown protein function using metabolite cocktail screening. Structure, 20, 1715-1725. PubMed id: 22940582

Date:

03-May-11 Release date: 22-Jun-11

Protein chain

Q9X024  (NNR_THEMA) -  Bifunctional NAD(P)H-hydrate repair enzyme Nnr from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 490 a.a.

Struc: 489 a.a.

Enzyme reactions

• Enzyme class 1: E.C.4.2.1.136 - ADP-dependent NAD(P)H-hydrate dehydratase.
• Reaction:
  1. (6S)-NADHX + ADP = AMP + phosphate + NADH + H⁺
  2. (6S)-NADPHX + ADP = AMP + phosphate + NADPH + H⁺

(6S)-NADHX + ADP = AMP + phosphate + NADH (Bound ligand (Het Group name = NAD) matches with 81.82% similarity) + H(+)

(6S)-NADPHX + ADP (Bound ligand (Het Group name = NAD) matches with 75.00% similarity) = AMP + phosphate + NADPH + H(+)

• Enzyme class 2: E.C.5.1.99.6 - NAD(P)H-hydrate epimerase.
• Reaction:
  1. (6R)-NADHX = (6S)-NADHX
  2. (6R)-NADPHX = (6S)-NADPHX

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Structure 20:1715-1725 (2012)

PubMed id: 22940582

Identification of unknown protein function using metabolite cocktail screening.

I.A.Shumilin, M.Cymborowski, O.Chertihin, K.N.Jha, J.C.Herr, S.A.Lesley, A.Joachimiak, W.Minor.

ABSTRACT

Proteins of unknown function comprise a significant fraction of sequenced genomes. Defining the roles of these proteins is vital to understanding cellular processes. Here, we describe a method to determine a protein function based on the identification of its natural ligand(s) by the crystallographic screening of the binding of a metabolite library, followed by a focused search in the metabolic space. The method was applied to two protein families with unknown function, PF01256 and YjeF_N. The PF01256 proteins, represented by YxkO from Bacillus subtilis and the C-terminal domain of Tm0922 from Thermotoga maritima, were shown to catalyze ADP/ATP-dependent NAD(P)H-hydrate dehydratation, a previously described orphan activity. The YjeF_N proteins, represented by mouse apolipoprotein A-I binding protein and the N-terminal domain of Tm0922, were found to interact with an adenosine diphosphoribose-related substrate and likely serve as ADP-ribosyltransferases. Crystallographic screening of metabolites serves as an efficient tool in functional analyses of uncharacterized proteins.