PDBsum entry 1vfl

Hydrolase

PDB id

1vfl

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Contents

			Protein chain

					349 a.a. *

			Metals

					_ZN

			Waters ×246

* Residue conservation analysis

PDB id:

1vfl

Links
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Name:

Hydrolase

Title:

Adenosine deaminase

Structure:

Adenosine deaminase. Chain: a. Ec: 3.5.4.4

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: intestine

Resolution:

1.80Å

R-factor:

0.240

R-free:

0.267

Authors:

T.Kinoshita

Key ref:

T.Kinoshita et al. (2005). Structural basis of compound recognition by adenosine deaminase. Biochemistry, 44, 10562-10569. PubMed id: 16060665 DOI: 10.1021/bi050529e

Date:

16-Apr-04

Release date:

16-Aug-05

PROCHECK

	Headers

	References

Protein chain

P56658 (ADA_BOVIN) - Adenosine deaminase from Bos taurus

Seq: Struc:					363 a.a. 349 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 15 residue positions (black crosses)



		Enzyme reactions

Enzyme class:

E.C.3.5.4.4 - adenosine deaminase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

1.	adenosine + H2O + H⁺ = inosine + NH4⁺
2.	2'-deoxyadenosine + H2O + H⁺ = 2'-deoxyinosine + NH4⁺

adenosine	+	H2O	+	H(+)	=	inosine	+	NH4(+)

2'-deoxyadenosine	+	H2O	+	H(+)	=	2'-deoxyinosine	+	NH4(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi050529e	Biochemistry 44:10562-10569 (2005)
PubMed id: 16060665

Structural basis of compound recognition by adenosine deaminase.
T.Kinoshita, I.Nakanishi, T.Terasaka, M.Kuno, N.Seki, M.Warizaya, H.Matsumura, T.Inoue, K.Takano, H.Adachi, Y.Mori, T.Fujii.

ABSTRACT

Structural snapshots corresponding to various states enable elucidation of the molecular recognition mechanism of enzymes. Adenosine deaminase has two distinct conformations, an open form and a closed form, although it has so far been unclear what factors influence adaptation of the alternative conformations. Herein, we have determined the first nonligated structure as an initial state, which was the open form, and have thereby rationally deduced the molecular recognition mechanism. Inspection of the active site in the nonligated and ligated states indicated that occupancy at one of the water-binding positions in the nonligated state was highly significant in determining alternate conformations. When this position is empty, subsequent movement of Phe65 toward the space induces the closed form. On the other hand, while occupied, the overall conformation remains in the open form. This structural understanding should greatly assist structure-oriented drug design and enable control of the enzymatic activity.

Literature references that cite this PDB file's key reference

PubMed id

Reference

18602399

E.T.Larson, W.Deng, B.E.Krumm, A.Napuli, N.Mueller, W.C.Van Voorhis, F.S.Buckner, E.Fan, A.Lauricella, G.DeTitta, J.Luft, F.Zucker, W.G.Hol, C.L.Verlinde, and E.A.Merritt (2008).
Structures of substrate- and inhibitor-bound adenosine deaminase from a human malaria parasite show a dramatic conformational change and shed light on drug selectivity.

J Mol Biol, 381, 975-988.

PDB codes:

2pgf 2pgr 2qvn

17379970

T.Kinoshita (2007).
[Application and development of structure-based drug design using X-ray analysis]

Nippon Yakurigaku Zasshi, 129, 186-190.

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.