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PDBsum entry 1kyh
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Structural genomics, unknown function PDB id
1kyh

 

 

 

 

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Contents
Protein chain
268 a.a. *
Waters ×209
* Residue conservation analysis
PDB id:
1kyh
Name: Structural genomics, unknown function
Title: Structure of bacillus subtilis yxko, a member of the upf0031 family and a putative kinase
Structure: Hypothetical 29.9 kda protein in sigy-cydd intergenic region. Chain: a. Engineered: yes
Source: Bacillus subtilis. Organism_taxid: 1423. Gene: yxko. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.60Å     R-factor:   0.228     R-free:   0.232
Authors: R.Zhang,I.Dementieva,E.Vinokour,F.Collart,A.Joachimiak,Midwest Center For Structural Genomics (Mcsg)
Key ref: R.G.Zhang et al. (2002). Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase. J Struct Biol, 139, 161-170. PubMed id: 12457846 DOI: 10.1016/S1047-8477(02)00532-4
Date:
04-Feb-02     Release date:   14-Aug-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P94368  (NNRD_BACSU) -  ADP-dependent (S)-NAD(P)H-hydrate dehydratase from Bacillus subtilis (strain 168)
Seq:
Struc: 		276 a.a.
268 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.4.2.1.136  - ADP-dependent NAD(P)H-hydrate dehydratase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. (6S)-NADHX + ADP = AMP + phosphate + NADH + H+
2. (6S)-NADPHX + ADP = AMP + phosphate + NADPH + H+
(6S)-NADHX
 + ADP
 = AMP
 + phosphate
 + NADH
 + H(+)
(6S)-NADPHX
 + ADP
 = AMP
 + phosphate
 + NADPH
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S1047-8477(02)00532-4 J Struct Biol 139:161-170 (2002)
PubMed id: 12457846  
 
 
Structure of Bacillus subtilis YXKO--a member of the UPF0031 family and a putative kinase.
R.G.Zhang, J.Grembecka, E.Vinokour, F.Collart, I.Dementieva, W.Minor, A.Joachimiak.
 
  ABSTRACT  
 
We determined the 1.6-A resolution crystal structure of a conserved hypothetical 29.9-kDa protein from the SIGY-CYDD intergenic region encoded by a Bacillus subtilis open reading frame in the YXKO locus. YXKO homologues are broadly distributed and are by and large described as proteins with unknown function. The YXKO protein has an alpha/beta fold and shows high structural homology to the members of a ribokinase-like superfamily. However, YXKO is the only member of this superfamily known to form tetramers. Putative binding sites for adenosine triphosphate (ATP), a substrate, and Mg(2+)-binding sites were revealed in the structure of the protein, based on high structural similarity to ATP-dependent members of the superfamily. Two adjacent monomers contribute residues to the active site. The crystal structure provides valuable information about the YXKO protein's tertiary and quaternary structure, the biochemical function of YXKO and its homologues, and the evolution of its ribokinase-like superfamily.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
  18097102 Y.F.Zhou, L.F.Li, C.Yang, Y.H.Liang, and X.D.Su (2008).
Preliminary X-ray crystallographic analysis of SMU.573, a putative sugar kinase from Streptococcus mutans.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 47-49.  
17702456 D.Ulanova, V.Holanová, L.Prenosilová, J.Náprstek, and I.Lichá (2007).
Mutation of a gene encoding a putative ribokinase leads to reduced salt tolerance under potassium limitation in Bacillus subtilis.
  Folia Microbiol (Praha), 52, 203-208.  
17242506 Y.Zhang, M.H.El Kouni, and S.E.Ealick (2007).
Substrate analogs induce an intermediate conformational change in Toxoplasma gondii adenosine kinase.
  Acta Crystallogr D Biol Crystallogr, 63, 126-134.
PDB codes: 2a9y 2a9z 2aa0 2ab8
16929110 L.Arnfors, T.Hansen, P.Schönheit, R.Ladenstein, and W.Meining (2006).
Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.
  Acta Crystallogr D Biol Crystallogr, 62, 1085-1097.
PDB codes: 2c49 2c4e
16287087 Y.Qiu, V.Tereshko, Y.Kim, R.Zhang, F.Collart, M.Yousef, A.Kossiakoff, and A.Joachimiak (2006).
The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold.
  Proteins, 62, 8.
PDB code: 1r4v
16421444 Y.Zhang, M.H.El Kouni, and S.E.Ealick (2006).
Structure of Toxoplasma gondii adenosine kinase in complex with an ATP analog at 1.1 angstroms resolution.
  Acta Crystallogr D Biol Crystallogr, 62, 140-145.
PDB code: 2abs
16233902 B.Nocek, C.Chang, H.Li, L.Lezondra, D.Holzle, F.Collart, and A.Joachimiak (2005).
Crystal structures of delta1-pyrroline-5-carboxylate reductase from human pathogens Neisseria meningitides and Streptococcus pyogenes.
  J Mol Biol, 354, 91.
PDB codes: 1yqg 2ag8 2ahr 2amf
15593246 F.J.Stevens, C.Kuemmel, G.Babnigg, and F.R.Collart (2005).
Efficient recognition of protein fold at low sequence identity by conservative application of Psi-BLAST: application.
  J Mol Recognit, 18, 150-157.  
15263850 Y.Kim, I.Dementieva, M.Zhou, R.Wu, L.Lezondra, P.Quartey, G.Joachimiak, O.Korolev, H.Li, and A.Joachimiak (2004).
Automation of protein purification for structural genomics.
  J Struct Funct Genomics, 5, 111-118.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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