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PDBsum entry 3rtd

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protein ligands metals links
Lyase PDB id
3rtd
Jmol
Contents
Protein chain
489 a.a.
Ligands
ALA-ALA-TRP-LEU-
PHE-GLU-ALA
NAI
ADP
NAX
Metals
__K
_MG
Waters ×70
PDB id:
3rtd
Name: Lyase
Title: Crystal structure of tm0922, a fusion of a domain of unknown and adp/atp-dependent NAD(p)h-hydrate dehydratase from ther maritima soaked with nadh and adp.
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: 562. Other_details: unknown peptide, probably from expression ho
Resolution:
2.30Å     R-factor:   0.167     R-free:   0.219
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 DOI: 10.1016/j.str.2012.07.016
Date:
03-May-11     Release date:   22-Jun-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9X024  (NNR_THEMA) -  Bifunctional NAD(P)H-hydrate repair enzyme Nnr
Seq:
Struc:
490 a.a.
489 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class 1: E.C.4.2.1.136  - ADP-dependent NAD(P)H-hydrate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. ADP + (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine- dinucleotide = AMP + phosphate + NADH
2. ADP + (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine- dinucleotide phosphate = AMP + phosphate + NADPH
ADP
+ (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine- dinucleotide
=
AMP
Bound ligand (Het Group name = NAI)
matches with 75.00% similarity
+ phosphate
+
NADH
Bound ligand (Het Group name = NAX)
matches with 97.78% similarity
ADP
+ (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide adenine- dinucleotide phosphate
= AMP
+ phosphate
+ NADPH
   Enzyme class 2: E.C.5.1.99.6  - NAD(P)H-hydrate epimerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. (6R)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = (6S)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide
2. (6R)-6-beta-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = (6S)-6-beta-hydroxy-1,4,5,6- tetrahydronicotinamide-adenine dinucleotide phosphate
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
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   1 term 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2012.07.016 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.