General Information

Database accession: MF7000546

Name: MT-ADPRase with ADPR

PDB ID: 1mk1 PDBe

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 PubMed

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

Function and Biology 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 GeneOntology

bis(5'-adenosyl)-pentaphosphatase activity bis(5'-adenosyl)-pentaphosphatase activity GeneOntology

guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity GeneOntology

manganese ion binding manganese ion binding GeneOntology

UDP-sugar diphosphatase activity UDP-sugar diphosphatase activity GeneOntology

Biological process:

nucleoside phosphate metabolic process nucleoside phosphate metabolic process GeneOntology

ribose phosphate metabolic process ribose phosphate metabolic process GeneOntology

Cellular component:

cytosol cytosol GeneOntology

Structure Summary 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


Chain A

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) UniProt

Coverage: 97%

Position :
0
Zoom :
x 1
FETISSETLHTGAIFALRRDQVRMPGGGIVTREVVEHFGAVAIVAMDDNGNIPMVYQYRHTYGRRLWELPAGLLDVAGEPPHLTAARELREEVGLQASTWQVLVDLDTAPGFSDESVRVYLATGLREVGRPEAHHEEADMTMGWYPIAEAARRVLRGEIVNSIAIAGVLAVHAVTTGFAQPRPLDTEWIDRPTAFAARRAER20406080100120140160180200Residues that have atomic coordinates in the PDB file.helicalhelical NUDIX domain (PF00293)SequenceSolved structureSecondary Struct.Pfam

Chain A-2

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) UniProt

Coverage: 97%

Position :
0
Zoom :
x 1
FETISSETLHTGAIFALRRDQVRMPGGGIVTREVVEHFGAVAIVAMDDNGNIPMVYQYRHTYGRRLWELPAGLLDVAGEPPHLTAARELREEVGLQASTWQVLVDLDTAPGFSDESVRVYLATGLREVGRPEAHHEEADMTMGWYPIAEAARRVLRGEIVNSIAIAGVLAVHAVTTGFAQPRPLDTEWIDRPTAFAARRAER20406080100120140160180200Residues that have atomic coordinates in the PDB file. NUDIX domain (PF00293)SequenceSolved structureSecondary Struct.Pfam

Evidence 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:

Related Structure(s) 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).

There are 38 related structures in the MFIB database:






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