Database accession: MF7000561
Name: ADP compounds hydrolase
PDB ID: 1vhg
Experimental method: X-ray (2.70 Å)
Assembly: Homodimer
Source organism: Escherichia coli
Primary publication of the structure:
Badger J, Sauder JM, Adams JM, Antonysamy S, Bain K, Bergseid MG, Buchanan SG, Buchanan MD, Batiyenko Y, Christopher JA, Emtage S, Eroshkina A, Feil I, Furlong EB, Gajiwala KS, Gao X, He D, Hendle J, Huber A, Hoda K, Kearins P, Kissinger C, Laubert B, Lewis HA, Lin J, Loomis K, Lorimer D, Louie G, Maletic M, Marsh CD, Miller I, Molinari J, Muller-Dieckmann HJ, Newman JM, Noland BW, Pagarigan B, Park F, Peat TS, Post KW, Radojicic S, Ramos A, Romero R, Rutter ME, Sanderson WE, Schwinn KD, Tresser J, Winhoven J, Wright TA, Wu L, Xu J, Harris TJ
Structural analysis of a set of proteins resulting from a bacterial genomics project.
(2005) Proteins 60: 787-96
PMID: 16021622
Abstract:
The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
ADP-ribose diphosphatase activity ADP-ribose diphosphatase activity
ADP-sugar diphosphatase activity ADP-sugar diphosphatase activity
magnesium ion binding magnesium ion binding
protein homodimerization activity protein homodimerization activity
Biological process:
nucleoside phosphate metabolic process nucleoside phosphate metabolic process
ribose phosphate metabolic process ribose phosphate metabolic process
Cellular component:
cytosol cytosol
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: ADP compounds hydrolase NudE
Source organism: Escherichia coli
Length: 186 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSKSLQKPTILNVETVARSRLFTVESVDLEFSNGVRRVYERMRPTNREAVMIVPIVDDHLILIREYAVGTESYELGFSKGLIDPGESVYEAANRELKEEVGFGANDLTFLKKLSMAPSYFSSKMNIVVAQDLYPESLEGDEPEPLPQVRWPLAHMMDLLEDPDFNEARNVSALFLVREWLKGQGRV
UniProtKB AC: P45799 (positions: 2-186)
Coverage: 99%
Name: ADP compounds hydrolase NudE
Source organism: Escherichia coli
Length: 186 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMSKSLQKPTILNVETVARSRLFTVESVDLEFSNGVRRVYERMRPTNREAVMIVPIVDDHLILIREYAVGTESYELGFSKGLIDPGESVYEAANRELKEEVGFGANDLTFLKKLSMAPSYFSSKMNIVVAQDLYPESLEGDEPEPLPQVRWPLAHMMDLLEDPDFNEARNVSALFLVREWLKGQGRV
UniProtKB AC: P45799 (positions: 2-186)
Coverage: 99%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: NUDIX domain
Evidence level: Indirect evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
The authors claim that ADP-ribose pyrophosphatase forms a symmetric homodimer, wherein the two catalytic sites are formed by residues of both monomers, requiring dimerization through domain swapping for substrate recognition and catalytic activity (PMID:11323725). E. coli ADPRase elutes as a dimer in gel exclusion chromatography (PMID:11323725). The N-terminal subdomain (residues 1-54) mediates dimerization and is a strong candidate for MSF, while the C-terminal one is a folded Nudix domain. Other structures belonging to the same domain type also show features implying MSF: large relative interface, domain swapping and a lack of the monomeric form in gel filtration experiments (PMID:12906832, PMID:15210687).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
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