PDBsum entry 1r4l

Hydrolase

PDB id: 1r4l

Contents

Protein chains

597 a.a. *

20 a.a. *

18 a.a. *

14 a.a. *

Ligands

UNK-UNK-UNK-UNK-UNK-UNK

NAG ×2

XX5

Metals

_CL

_ZN

Waters ×13

* Residue conservation analysis

PDB id:

1r4l

Name:

Hydrolase

Title:

Inhibitor bound human angiotensin converting enzyme-related carboxypeptidase (ace2)

Structure:

Angiotensin i converting enzyme 2. Chain: a. Fragment: extracellular domains. Synonym: angiotensin converting enzyme-like protein, angiotensin converting enzyme-related carboxypeptidase. Engineered: yes. Disordered segment of collectrin homology domain. Chain: b. Engineered: yes.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ace2. Expressed in: spodoptera frugiperda. Expression_system_taxid: 7108. Expression_system_cell_line: sf9.

Resolution:

3.00Å R-factor: 0.253 R-free: 0.337

Authors:

P.Towler,B.Staker,S.G.Prasad,S.Menon,D.Ryan,J.Tang,T.Parsons, M.Fisher,D.Williams,N.A.Dales,M.A.Patane,M.W.Pantoliano

Key ref:

P.Towler et al. (2004). ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis. J Biol Chem, 279, 17996-18007. PubMed id: 14754895 DOI: 10.1074/jbc.M311191200

Date:

07-Oct-03 Release date: 03-Feb-04

Protein chain

Q9BYF1  (ACE2_HUMAN) -  Angiotensin-converting enzyme 2 from Homo sapiens

Seq: 805 a.a.

Struc: 597 a.a.

Protein chain

No UniProt id for this chain

Struc: 20 a.a.

Protein chain

No UniProt id for this chain

Struc: 18 a.a.

Protein chain

No UniProt id for this chain

Struc: 14 a.a.

Enzyme reactions

• Enzyme class 2: Chain A: E.C.3.4.17.- - ?????
• Enzyme class 3: Chain A: E.C.3.4.17.23 - angiotensin-converting enzyme 2.
• Reaction: angiotensin II + H2O = angiotensin-^1-7 + L-phenylalanine

angiotensin II + H2O = angiotensin-(1-7) + L-phenylalanine (Bound ligand (Het Group name = NAG) matches with 44.44% similarity)

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

Added reference

DOI no: 10.1074/jbc.M311191200

J Biol Chem 279:17996-18007 (2004)

PubMed id: 14754895

ACE2 X-ray structures reveal a large hinge-bending motion important for inhibitor binding and catalysis.

P.Towler, B.Staker, S.G.Prasad, S.Menon, J.Tang, T.Parsons, D.Ryan, M.Fisher, D.Williams, N.A.Dales, M.A.Patane, M.W.Pantoliano.

ABSTRACT

The angiotensin-converting enzyme (ACE)-related carboxypeptidase, ACE2, is a type I integral membrane protein of 805 amino acids that contains one HEXXH + E zinc-binding consensus sequence. ACE2 has been implicated in the regulation of heart function and also as a functional receptor for the coronavirus that causes the severe acute respiratory syndrome (SARS). To gain further insights into this enzyme, the first crystal structures of the native and inhibitor-bound forms of the ACE2 extracellular domains were solved to 2.2- and 3.0-A resolution, respectively. Comparison of these structures revealed a large inhibitor-dependent hinge-bending movement of one catalytic subdomain relative to the other ( approximately 16 degrees ) that brings important residues into position for catalysis. The potent inhibitor MLN-4760 ((S,S)-2-[1-carboxy-2-[3-(3,5-dichlorobenzyl)-3H-imidazol4-yl]-ethylamino]-4-methylpentanoic acid) makes key binding interactions within the active site and offers insights regarding the action of residues involved in catalysis and substrate specificity. A few active site residue substitutions in ACE2 relative to ACE appear to eliminate the S(2)' substrate-binding subsite and account for the observed reactivity change from the peptidyl dipeptidase activity of ACE to the carboxypeptidase activity of ACE2.

Selected figure(s)

Figure 4.
FIG. 4. Superposition of the native and inhibitor-bound ACE2 structures. A, the 409 -carbon atoms corresponding to subdomain II of the native and inhibitor-bound ACE2 structures were superimposed with an r.m.s. deviation of 1.41 Å. Native ACE2 is colored red, and inhibitor-bound ACE2 is colored green. The zinc ion is shown as a yellow sphere, and the inhibitor MLN-4760 is shown in a ball-and-stick rendering with default atom coloring: gray, carbon; blue, nitrogen; red, oxygen; green, chlorine. This view is looking down the length of the active site cleft and is rotated 90° from that shown in Fig. 3. This perspective illustrates the 16° hinge-bending movement of subdomain I relative to subdomain II that occurs upon inhibitor binding to ACE2. B, shown is a close-up view of the active sites of the superimposed native (red) and inhibitor-bound (green) ACE2 structures. This is the same superposition of subdomain II for both structures as described for A. In this perspective, the residues of subdomain I within the active site are shown to move upon inhibitor binding relative to those in subdomain II. The inhibitor MLN-4760 is shown in stick rendering with the same atom color code as described for A. The average movement for residues near the active site is 6-9 Å. The yellow spheres are the two positions of the zinc atom in the native and inhibitor-bound structures. This figure was prepared using MOE 2003.02 software (Chemical Computing Group, Inc.).

Figure 6.
FIG. 6. Superposition of the ACE2 and tACE structures. A, the -carbon atoms in lisinopril-bound tACE (13) were superimposed onto the equivalent atoms in inhibitor-bound ACE2 (588 residues) with an r.m.s. deviation of 1.80 Å. MLN-4760-bound ACE2 is magenta, and lisinopril-bound tACE is green. MLN-4760 is shown bound to ACE2 with the same color code described in the legend to Fig. 4A. Similarly, the zinc and chloride ions are shown as described in the legend to Fig. 3. The orientation is the same as that shown for native ACE2 in Fig. 3. Structures were superimposed using MOE 2003.02 software. B, the 21 -carbon atoms at the inhibitor-bound active site of ACE2 (residues 4.5 Å from the inhibitor) were superimposed onto the equivalent atoms of lisinopril-bound tACE (Protein Data Bank code 1O86 [PDB] ) with an r.m.s. deviation of 0.53 Å. The active site of ACE2 and MLN-4760 are shown in default colors, with the inhibitor displayed in stick rendering. Labels are for ACE2 residues only. The active site residues of tACE are shown in orange, with the inhibitor lisinopril colored purple in stick rendering. The zinc ion is shown as a yellow sphere, and the second chloride ion of tACE (CL2) is shown as an orange sphere. This chloride ion site does not exist in ACE2 due to the Glu398 substitution for Pro407 (see "Results and Discussion"). Other important differences between ACE2 and tACE are as follows: Arg273 versus Gln281, Phe^274 versus Thr282, and Tyr510 versus Val518, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 17996-18007) copyright 2004.

Figures were selected by the author.

Author's comment

One interesting feature of this zinc metallopeptidase is the large hinge-bending conformation change that occurs upon inhibitor (and presumably also substrate) binding. A similar conformational change is believed to occur for inhibitor and substrate binding to the closest homologs of ACE2: testicular and somatic ACE. These enzymes are all now believed to play critical roles in the renin angiotensin system for bood pressure homeostasis.
Another interesting feature of ACE2 is the discovery that it has been high jacked to serve as the functional receptor of the SARS coronovirus (Li et al. 2003, Nature 426, 450-454). However, inhibitors of ACE2 such as MLN-4760, shown bound to the active site in these crystal structures, do not block binding of the virus. The reason for this became apparent after publication of the structure of the SARS coronovirus spike protein bound to ACE2 (see Li, et al. 2005, SCIENCE 309, p1864-1868). This paper revealed that the virus binds to the N-terminal lobe of the peptidase, far removed from the peptidase catalytic center.
Michael W. Pantoliano