Database accession: MF7000546
Name: MT-ADPRase with ADPR
PDB ID: 1mk1
Experimental method: X-ray (2.00 Å)
Assembly: Homodimer
Source organism: Mycobacterium tuberculosis
Primary publication of the structure:
Kang LW, Gabelli SB, Cunningham JE, O'Handley SF, Amzel LM
Structure and mechanism of MT-ADPRase, a nudix hydrolase from Mycobacterium tuberculosis.
(2003) Structure 11: 1015-23
PMID: 12906832
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
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
ADP-sugar diphosphatase activity ADP-sugar diphosphatase activity
bis(5'-adenosyl)-pentaphosphatase activity bis(5'-adenosyl)-pentaphosphatase activity
guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity
manganese ion binding manganese ion binding
UDP-sugar diphosphatase activity UDP-sugar diphosphatase 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, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: MutT/nudix family protein
Source organism: Mycobacterium tuberculosis
Length: 207 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAEHDFETISSETLHTGAIFALRRDQVRMPGGGIVTREVVEHFGAVAIVAMDDNGNIPMVYQYRHTYGRRLWELPAGLLDVAGEPPHLTAARELREEVGLQASTWQVLVDLDTAPGFSDESVRVYLATGLREVGRPEAHHEEADMTMGWYPIAEAARRVLRGEIVNSIAIAGVLAVHAVTTGFAQPRPLDTEWIDRPTAFAARRAER
UniProtKB AC: O33199 (positions: 6-207)
Coverage: 97%
Name: MutT/nudix family protein
Source organism: Mycobacterium tuberculosis
Length: 207 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMAEHDFETISSETLHTGAIFALRRDQVRMPGGGIVTREVVEHFGAVAIVAMDDNGNIPMVYQYRHTYGRRLWELPAGLLDVAGEPPHLTAARELREEVGLQASTWQVLVDLDTAPGFSDESVRVYLATGLREVGRPEAHHEEADMTMGWYPIAEAARRVLRGEIVNSIAIAGVLAVHAVTTGFAQPRPLDTEWIDRPTAFAARRAER
UniProtKB AC: O33199 (positions: 6-207)
Coverage: 97%
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 A-2:
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)
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