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PDBsum entry 1mr2
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protein ligands metals links
Hydrolase PDB id
1mr2

 

 

 

 

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Contents
Protein chain
187 a.a. *
Ligands
A12
Metals
_MN
Waters ×58
* Residue conservation analysis
PDB id:
1mr2
Name: Hydrolase
Title: Structure of the mt-adprase in complex with 1 mn2+ ion and amp-cp (a inhibitor), a nudix enzyme
Structure: Adpr pyrophosphatase. Chain: a. Synonym: adprase, mutt/nudix family protein, hypothetical protein rv1700. Engineered: yes
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: rv1700. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.205     R-free:   0.260
Authors: L.-W.Kang,S.B.Gabelli,M.A.Bianchet,J.E.Cunningham,S.F.O'Handley, L.M.Amzel
Key ref:
L.W.Kang et al. (2003). Structure and mechanism of MT-ADPRase, a nudix hydrolase from Mycobacterium tuberculosis. Structure, 11, 1015-1023. PubMed id: 12906832 DOI: 10.1016/S0969-2126(03)00154-0
Date:
17-Sep-02     Release date:   05-Aug-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
O33199  (O33199_MYCTO) -  MutT/nudix family protein from Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
Seq:
Struc: 		207 a.a.
187 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.6.1.13  - ADP-ribose diphosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ADP-D-ribose + H2O = D-ribose 5-phosphate + AMP + 2 H+
ADP-D-ribose
 + H2O
 =
D-ribose 5-phosphate
Bound ligand (Het Group name = A12)
matches with 78.57% similarity 		+ AMP
 + 2 × H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(03)00154-0 Structure 11:1015-1023 (2003)
PubMed id: 12906832  
 
 
Structure and mechanism of MT-ADPRase, a nudix hydrolase from Mycobacterium tuberculosis.
L.W.Kang, S.B.Gabelli, J.E.Cunningham, S.F.O'Handley, L.M.Amzel.
 
  ABSTRACT  
 
Nudix hydrolases are a family of proteins that contain the characteristic sequence GX(5)EX(7)REUXEEXG(I/L/V), the Nudix box. They catalyze the hydrolysis of a variety of nucleoside diphosphate derivatives such as ADP-ribose, Ap(n)A (3 </= n </= 6), NADH, and dATP. A number of Nudix hydrolases from several species, ranging from bacteria to humans, have been characterized, including, in some cases, the determination of their three-dimensional structures. The product of the Rv1700 gene of M. tuberculosis is a Nudix hydrolase specific for ADP-ribose (ADPR). We have determined the crystal structures of MT-ADPRase alone, and in complex with substrate, with substrate and the nonactivating metal ion Gd(3+), and in complex with a nonhydrolyzable ADPR analog and the activating metal ion Mn(2+). These structures, refined with data extending to resolutions between 2.0 and 2.3 A, showed that there are sequence differences in binding site residues between MT-ADPRase and a human homolog that may be exploited for antituberculosis drug development.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Recognition of the Nonhydrolyzable Substrate Analog, AMPCPR, and Three Mn2+ Ions by MT-ADPRase(A) Schematic representation. Residue 142 is from loop L9 that is not ordered without three manganese ions and AMPCPR.(B) Stereo diagram of the ADP-ribose binding site with AMPCPR and three manganese ions. Residues and substrate are shown using the same representation and color scheme of Figure 4A. Broken orange lines represent polar interactions among AMPCPR, three manganese ions, and protein residues.
 
  The above figure is reprinted by permission from Cell Press: Structure (2003, 11, 1015-1023) copyright 2003.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19864691 T.Nakamura, S.Meshitsuka, S.Kitagawa, N.Abe, J.Yamada, T.Ishino, H.Nakano, T.Tsuzuki, T.Doi, Y.Kobayashi, S.Fujii, M.Sekiguchi, and Y.Yamagata (2010).
Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base.
  J Biol Chem, 285, 444-452.
PDB codes: 3a6s 3a6t 3a6u 3a6v
19585659 A.G.Thorsell, C.Persson, S.Gräslund, M.Hammarström, R.D.Busam, and B.M.Hallberg (2009).
Crystal structure of human diphosphoinositol phosphatase 1.
  Proteins, 77, 242-246.
PDB codes: 2fvv 2q9p
19604474 N.Huang, J.De Ingeniis, L.Galeazzi, C.Mancini, Y.D.Korostelev, A.B.Rakhmaninova, M.S.Gelfand, D.A.Rodionov, N.Raffaelli, and H.Zhang (2009).
Structure and function of an ADP-ribose-dependent transcriptional regulator of NAD metabolism.
  Structure, 17, 939-951.
PDB codes: 3gz5 3gz6 3gz8
19278661 S.A.Messing, S.B.Gabelli, Q.Liu, H.Celesnik, J.G.Belasco, S.A.Piñeiro, and L.M.Amzel (2009).
Structure and biological function of the RNA pyrophosphohydrolase BdRppH from Bdellovibrio bacteriovorus.
  Structure, 17, 472-481.
PDB codes: 3ees 3eeu 3ef5 3ffu
18512963 G.W.Buchko, O.Litvinova, H.Robinson, A.F.Yakunin, and M.A.Kennedy (2008).
Functional and structural characterization of DR_0079 from Deinococcus radiodurans, a novel Nudix hydrolase with a preference for cytosine (deoxy)ribonucleoside 5'-Di- and triphosphates.
  Biochemistry, 47, 6571-6582.
PDB code: 2o5f
18275811 N.Huang, L.Sorci, X.Zhang, C.A.Brautigam, X.Li, N.Raffaelli, G.Magni, N.V.Grishin, A.L.Osterman, and H.Zhang (2008).
Bifunctional NMN adenylyltransferase/ADP-ribose pyrophosphatase: structure and function in bacterial NAD metabolism.
  Structure, 16, 196-209.
PDB codes: 2qjo 2qjt 2r5w
18039767 T.Wakamatsu, N.Nakagawa, S.Kuramitsu, and R.Masui (2008).
Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8.
  J Bacteriol, 190, 1108-1117.
PDB codes: 2yvm 2yvn 2yvo 2yvp
  17768363 J.Jung, Y.J.Ahn, and L.W.Kang (2007).
Overexpression, crystallization and preliminary X-ray crystallographic analysis of Nudix hydrolase Orf141 from Escherichia coli K-1.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 812-815.  
17698004 S.B.Gabelli, M.A.Bianchet, W.Xu, C.A.Dunn, Z.D.Niu, L.M.Amzel, and M.J.Bessman (2007).
Structure and function of the E. coli dihydroneopterin triphosphate pyrophosphatase: a Nudix enzyme involved in folate biosynthesis.
  Structure, 15, 1014-1022.
PDB codes: 2o1c 2o5w
17166279 A.K.Arakaki, W.Tian, and J.Skolnick (2006).
High precision multi-genome scale reannotation of enzyme function by EFICAz.
  BMC Genomics, 7, 315.  
16900379 D.I.Fisher, J.L.Cartwright, and A.G.McLennan (2006).
Characterization of the Mn2+-stimulated (di)adenosine polyphosphate hydrolase encoded by the Deinococcus radiodurans DR2356 nudix gene.
  Arch Microbiol, 186, 415-424.  
15995214 K.Okuda, H.Hayashi, and Y.Nishiyama (2005).
Systematic characterization of the ADP-ribose pyrophosphatase family in the Cyanobacterium Synechocystis sp. strain PCC 6803.
  J Bacteriol, 187, 4984-4991.  
15162484 G.W.Buchko, S.Ni, S.R.Holbrook, and M.A.Kennedy (2004).
Solution structure of hypothetical Nudix hydrolase DR0079 from extremely radiation-resistant Deinococcus radiodurans bacterium.
  Proteins, 56, 28-39.
PDB code: 1q27
15133035 M.Mishima, Y.Sakai, N.Itoh, H.Kamiya, M.Furuichi, M.Takahashi, Y.Yamagata, S.Iwai, Y.Nakabeppu, and M.Shirakawa (2004).
Structure of human MTH1, a Nudix family hydrolase that selectively degrades oxidized purine nucleoside triphosphates.
  J Biol Chem, 279, 33806-33815.
PDB code: 1iry
15274914 S.B.Gabelli, M.A.Bianchet, H.F.Azurmendi, Z.Xia, V.Sarawat, A.S.Mildvan, and L.M.Amzel (2004).
Structure and mechanism of GDP-mannose glycosyl hydrolase, a Nudix enzyme that cleaves at carbon instead of phosphorus.
  Structure, 12, 927-935.
PDB code: 1rya
15210687 S.Yoshiba, T.Ooga, N.Nakagawa, T.Shibata, Y.Inoue, S.Yokoyama, S.Kuramitsu, and R.Masui (2004).
Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.
  J Biol Chem, 279, 37163-37174.
PDB codes: 1v8i 1v8l 1v8m 1v8n 1v8r 1v8s 1v8t 1v8u 1v8v 1v8w 1v8y
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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