Linked Life Data

15003455

Source:http://linkedlifedata.com/resource/pubmed/id/15003455

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
2
pubmed:dateCreated
2004-3-8
pubmed:databankReference
pubmed:abstractText
Creatininase from Pseudomonas putida is a member of the urease-related amidohydrolase superfamily. The crystal structure of the Mn-activated enzyme has been solved by the single isomorphous replacement method at 1.8A resolution. The structures of the native creatininase and the Mn-activated creatininase-creatine complex have been determined by a difference Fourier method at 1.85 A and 1.6 A resolution, respectively. We found the disc-shaped hexamer to be roughly 100 A in diameter and 50 A in thickness and arranged as a trimer of dimers with 32 (D3) point group symmetry. The enzyme is a typical Zn2+ enzyme with a binuclear metal center (metal1 and metal2). Atomic absorption spectrometry and X-ray crystallography revealed that Zn2+ at metal1 (Zn1) was easily replaced with Mn2+ (Mn1). In the case of the Mn-activated enzyme, metal1 (Mn1) has a square-pyramidal geometry bound to three protein ligands of Glu34, Asp45, and His120 and two water molecules. Metal2 (Zn2) has a well-ordered tetrahedral geometry bound to the three protein ligands of His36, Asp45, and Glu183 and a water molecule. The crystal structure of the Mn-activated creatininase-creatine complex, which is the first structure as the enzyme-substrate/inhibitor complex of creatininase, reveals that significant conformation changes occur at the flap (between the alpha5 helix and the alpha6 helix) of the active site and the creatine is accommodated in a hydrophobic pocket consisting of Trp174, Trp154, Tyr121, Phe182, Tyr153, and Gly119. The high-resolution crystal structure of the creatininase-creatine complex enables us to identify two water molecules (Wat1 and Wat2) that are possibly essential for the catalytic mechanism of the enzyme. The structure and proposed catalytic mechanism of the creatininase are different from those of urease-related amidohydrolase superfamily enzymes. We propose a new two-step catalytic mechanism possibly common to creatininases in which the Wat1 acts as the attacking nucleophile in the water-adding step and the Wat2 acts as the catalytic acid in the ring-opening step.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Mar
pubmed:issn
0022-2836
pubmed:author
pubmed:issnType
Print
pubmed:day
19
pubmed:volume
337
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
399-416
pubmed:dateRevised
2008-11-21
pubmed:meshHeading
pubmed-meshheading:15003455-Amidohydrolases, pubmed-meshheading:15003455-Amino Acid Sequence, pubmed-meshheading:15003455-Binding Sites, pubmed-meshheading:15003455-Catalysis, pubmed-meshheading:15003455-Catalytic Domain, pubmed-meshheading:15003455-Creatine, pubmed-meshheading:15003455-Crystallography, X-Ray, pubmed-meshheading:15003455-Enzyme Stability, pubmed-meshheading:15003455-Hot Temperature, pubmed-meshheading:15003455-Metals, pubmed-meshheading:15003455-Models, Molecular, pubmed-meshheading:15003455-Molecular Sequence Data, pubmed-meshheading:15003455-Protein Conformation, pubmed-meshheading:15003455-Protein Structure, Quaternary, pubmed-meshheading:15003455-Protein Subunits, pubmed-meshheading:15003455-Pseudomonas putida, pubmed-meshheading:15003455-Sequence Homology, Amino Acid, pubmed-meshheading:15003455-Substrate Specificity
pubmed:year
2004
pubmed:articleTitle
Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism.
pubmed:affiliation
Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan. yosimoto@net.nagasaki-u.ac.jp
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't